Arduino Due upload firmware issue

I have Arduino Due on SAM3x8e. I'm on Ubuntu 14.04. Before today I uploaded firmware via terminal using those commands:

$ stty -F /dev/ttyACM0 speed 1200 cs8 -cstopb -parenb
$ /home/q/apps/devel/arduino/arduino-1.5.7/hardware/tools/bossac --port=ttyACM0 -U false -e -w -v -b /home/q/work/gk/j-v2/embedded/smib/Release/smib.bin -R

It was good, but now it stopped working. Bossac just hangs up '-d' displays nothing. That is all.

I downloaded arduino IDE 1.6.5, but this doesn't matter. In ide's console I get

Sketch uses 11,000 bytes (2%) of program storage space. Maximum is 524,288 bytes.
Forcing reset using 1200bps open/close on port /dev/ttyACM0
/home/q/.arduino15/packages/arduino/tools/bossac/1.3a-arduino/bossac -i -d --port=ttyACM0 -U false -e -w -v -b /tmp/build238086227206829290.tmp/AnalogReadSerial.cpp.bin -R

It sticks, no leds blinking on Arduino board. It seems it actually hangs up, due to it loads 99% of CPU... May be Ubuntu update caused this issue...?

dmesg

[ 5168.658692] usb 3-3: new full-speed USB device number 7 using xhci_hcd
[ 5168.676969] usb 3-3: New USB device found, idVendor=2341, idProduct=003d
[ 5168.676979] usb 3-3: New USB device strings: Mfr=1, Product=2, SerialNumber=220
[ 5168.676985] usb 3-3: Product: Arduino Due Prog. Port
[ 5168.676989] usb 3-3: Manufacturer: Arduino (www.arduino.cc)
[ 5168.676994] usb 3-3: SerialNumber: 75438313633351A07051
[ 5168.677225] usb 3-3: ep 0x82 - rounding interval to 1024 microframes, ep desc says 2040 microframes
[ 5168.677652] cdc_acm 3-3:1.0: ttyACM0: USB ACM device

syslog

Oct  4 21:49:01 4xybook kernel: [ 5356.553290] usb 3-3: new full-speed USB device number 8 using xhci_hcd
Oct  4 21:49:01 4xybook kernel: [ 5356.571623] usb 3-3: New USB device found, idVendor=2341, idProduct=003d
Oct  4 21:49:01 4xybook kernel: [ 5356.571635] usb 3-3: New USB device strings: Mfr=1, Product=2, SerialNumber=220
Oct  4 21:49:01 4xybook kernel: [ 5356.571643] usb 3-3: Product: Arduino Due Prog. Port
Oct  4 21:49:01 4xybook kernel: [ 5356.571649] usb 3-3: Manufacturer: Arduino (www.arduino.cc)
Oct  4 21:49:01 4xybook kernel: [ 5356.571655] usb 3-3: SerialNumber: 75438313633351A07051
Oct  4 21:49:01 4xybook kernel: [ 5356.571923] usb 3-3: ep 0x82 - rounding interval to 1024 microframes, ep desc says 2040 microframes
Oct  4 21:49:01 4xybook kernel: [ 5356.572506] cdc_acm 3-3:1.0: ttyACM0: USB ACM device
Oct  4 21:49:01 4xybook mtp-probe: checking bus 3, device 8: "/sys/devices/pci0000:00/0000:00:14.0/usb3/3-3"
Oct  4 21:49:01 4xybook mtp-probe: bus: 3, device: 8 was not an MTP device

lsusb

Bus 002 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 004: ID 8087:07da Intel Corp. 
Bus 001 Device 003: ID 064e:c336 Suyin Corp. 
Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 004 Device 002: ID 152d:0567 JMicron Technology Corp. / JMicron USA Technology Corp. 
Bus 004 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 003 Device 008: ID 2341:003d Arduino SA 
Bus 003 Device 002: ID 1a2c:0e24 China Resource Semico Co., Ltd 
Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

Any help would be really appreciated.

Update

strace gives this.

execve("/home/q/apps/devel/arduino/arduino-1.5.7/hardware/tools/bossac", ["/home/q/apps/devel/arduino/ardui"..., "--port=ttyACM0", "-U", "false", "-e", "-w", "-v", "-b", "-d", "/home/q/work/gamekeeper/jackpot-"..., "-R"], [/* 78 vars */]) = 0
brk(0)                                  = 0x22a5000
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f468e385000
access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or directory)
open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=169535, ...}) = 0
mmap(NULL, 169535, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f468e35b000
close(3)                                = 0
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
open("/usr/lib/x86_64-linux-gnu/libstdc++.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0 \266\5\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0644, st_size=979056, ...}) = 0
mmap(NULL, 3159040, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f468de61000
mprotect(0x7f468df47000, 2093056, PROT_NONE) = 0
mmap(0x7f468e146000, 40960, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0xe5000) = 0x7f468e146000
mmap(0x7f468e150000, 82944, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f468e150000
close(3)                                = 0
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
open("/lib/x86_64-linux-gnu/libgcc_s.so.1", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\260*\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0644, st_size=90080, ...}) = 0
mmap(NULL, 2185952, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f468dc4b000
mprotect(0x7f468dc61000, 2093056, PROT_NONE) = 0
mmap(0x7f468de60000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x15000) = 0x7f468de60000
close(3)                                = 0
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
open("/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\320\37\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=1840928, ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f468e35a000
mmap(NULL, 3949248, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f468d886000
mprotect(0x7f468da41000, 2093056, PROT_NONE) = 0
mmap(0x7f468dc40000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1ba000) = 0x7f468dc40000
mmap(0x7f468dc46000, 17088, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f468dc46000
close(3)                                = 0
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
open("/lib/x86_64-linux-gnu/libm.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\20V\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0644, st_size=1071552, ...}) = 0
mmap(NULL, 3166568, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f468d580000
mprotect(0x7f468d685000, 2093056, PROT_NONE) = 0
mmap(0x7f468d884000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x104000) = 0x7f468d884000
close(3)                                = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f468e359000
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f468e357000
arch_prctl(ARCH_SET_FS, 0x7f468e357780) = 0
mprotect(0x7f468dc40000, 16384, PROT_READ) = 0
mprotect(0x7f468d884000, 4096, PROT_READ) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f468e356000
mprotect(0x7f468e146000, 32768, PROT_READ) = 0
mprotect(0x7f468e387000, 4096, PROT_READ) = 0
munmap(0x7f468e35b000, 169535)          = 0
brk(0)                                  = 0x22a5000
brk(0x22c6000)                          = 0x22c6000
openat(AT_FDCWD, "/dev", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 3
open("/dev/ttyACM0", O_RDWR|O_NOCTTY|O_NONBLOCK) = 4
ioctl(4, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, {B9600 opost isig icanon echo ...}) = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, {B9600 opost isig icanon echo ...}) = 0
ioctl(4, SNDCTL_TMR_START or SNDRV_TIMER_IOCTL_TREAD or TCSETS, {B115200 -opost -isig -icanon -echo ...}) = 0
ioctl(4, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, {B115200 -opost -isig -icanon -echo ...}) = 0
nanosleep({0, 500000000}, NULL)         = 0
select(5, [4], NULL, NULL, {0, 100000}) = 1 (in [4], left {0, 99992})
read(4, "", 1024)                       = 0
select(5, [4], NULL, NULL, {0, 100000}) = 1 (in [4], left {0, 99994})
read(4, "", 1024)                       = 0
select(5, [4], NULL, NULL, {0, 100000}) = 1 (in [4], left {0, 99996})
read(4, "", 1024)                       = 0
select(5, [4], NULL, NULL, {0, 100000}) = 1 (in [4], left {0, 99997})
read(4, "", 1024)                       = 0
select(5, [4], NULL, NULL, {0, 100000}) = 1 (in [4], left {0, 99997})
read(4, "", 1024)                       = 0
select(5, [4], NULL, NULL, {0, 100000}) = 1 (in [4], left {0, 99997})
read(4, "", 1024)                       = 0

It indefinitely polls the descriptor. select = 1 means there is a data, but read returns 0. It seems like something on lower level is broken... may be because of system update (