issue with uploading sketch via programmer (sam-ice)

Hi,
I have an Elecrow Crowduino M0 SD and have some issues with uploading a sketch.

Environment:
- Arduino IDE 1.6.11 from arduino.cc
- Arduino SAMD Boards (32-bits ARM Cortex-M0+) 1.6.6 via Boardmanager
- Blink Sketch

I've flashed the bootloader with arduino IDE + programmer "ATMEL SAM-ICE". Works great:

```
C:\Users\\AppData\Local\Arduino15\packages\arduino\tools\openocd\0.9.0-arduino/bin/openocd.exe -d2 -s C:\Users\\AppData\Local\Arduino15\packages\arduino\tools\openocd\0.9.0-arduino/share/openocd/scripts/ -f C:\Users\\AppData\Local\Arduino15\packages\arduino\hardware\samd\1.6.6/variants/arduino_zero/openocd_scripts/arduino_zero.cfg -c telnet_port disabled; init; halt; at91samd bootloader 0; program {{C:\Users\\AppData\Local\Arduino15\packages\arduino\hardware\samd\1.6.6/bootloaders/zero/samd21_sam_ba.bin}} verify reset; shutdown
Open On-Chip Debugger 0.9.0-gd4b7679 (2015-06-10-22:24)
Licensed under GNU GPL v2
For bug reports, read
http://openocd.org/doc/doxygen/bugs.html
debug_level: 2
Info : only one transport option; autoselect 'swd'
adapter speed: 500 kHz
adapter_nsrst_delay: 100
cortex_m reset_config sysresetreq
Info : CMSIS-DAP: SWD Supported
Info : CMSIS-DAP: JTAG Supported
Info : CMSIS-DAP: Interface Initialised (SWD)
Info : CMSIS-DAP: FW Version = 01.21.0076
Info : SWCLK/TCK = 1 SWDIO/TMS = 1 TDI = 1 TDO = 1 nTRST = 0 nRESET = 1
Info : CMSIS-DAP: Interface ready
Info : clock speed 500 kHz
Info : SWD IDCODE 0x0bc11477
Info : at91samd21g18.cpu: hardware has 4 breakpoints, 2 watchpoints
target state: halted
target halted due to debug-request, current mode: Thread
xPSR: 0x61000000 pc: 0x000041b6 msp: 0x20007fe8
target state: halted
target halted due to debug-request, current mode: Thread
xPSR: 0x61000000 pc: 0x000005e8 msp: 0x20007ffc
** Programming Started **
auto erase enabled
Info : SAMD MCU: SAMD21G18A (256KB Flash, 32KB RAM)
wrote 16384 bytes from file C:\Users\\AppData\Local\Arduino15\packages\arduino\hardware\samd\1.6.6/bootloaders/zero/samd21_sam_ba.bin in 1.898500s (8.428 KiB/s)
** Programming Finished **
** Verify Started **
verified 5972 bytes in 0.521500s (11.183 KiB/s)
** Verified OK **
** Resetting Target **
shutdown command invoked
```

Uploading a sketch via USB works also:

```
Der Sketch verwendet 8.356 Bytes (3%) des Programmspeicherplatzes. Das Maximum sind 262.144 Bytes.
Erzwinge Reset durch öffnen/schließen mit 1200 bps auf dem Port COM12
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
PORTS {COM12, } / {COM12, } => {}
Uploading using selected port: COM12
C:\Users\\AppData\Local\Arduino15\packages\arduino\tools\bossac\1.6.1-arduino/bossac.exe -i -d --port=COM12 -U true -i -e -w -v C:\Users\\AppData\Local\Temp\buildbb61b02d674ae2bfb0845dfb247346a1.tmp/Blink.ino.bin -R
Set binary mode
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
version()=v2.0 [Arduino:XYZ] May 9 2016 16:06:46
chipId=0x10010005
Connected at 921600 baud
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
Atmel SMART device 0x10010005 found
write(addr=0x20004000,size=0x34)
writeWord(addr=0x20004030,value=0x10)
writeWord(addr=0x20004020,value=0x20008000)
Device : ATSAMD21G18A
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
Chip ID : 10010005
version()=v2.0 [Arduino:XYZ] May 9 2016 16:06:46
Version : v2.0 [Arduino:XYZ] May 9 2016 16:06:46
Address : 8192
Pages : 3968
Page Size : 64 bytes
Total Size : 248KB
Planes : 1
Lock Regions : 16
Locked : readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
readWord(addr=0x41004020)=0xffff
none
readWord(addr=0x41004018)=0
Security : false
Boot Flash : true
readWord(addr=0x40000834)=0x7000a
BOD : true
readWord(addr=0x40000834)=0x7000a
BOR : true
Arduino : FAST_CHIP_ERASE
Arduino : FAST_MULTI_PAGE_WRITE
Arduino : CAN_CHECKSUM_MEMORY_BUFFER
Erase flash
chipErase(addr=0x2000)
done in 0.807 seconds

Write 8508 bytes to flash (133 pages)
write(addr=0x20005000,size=0x1000)
writeBuffer(scr_addr=0x20005000, dst_addr=0x2000, size=0x1000)

[============== ] 48% (64/133 pages)write(addr=0x20005000,size=0x1000)
writeBuffer(scr_addr=0x20005000, dst_addr=0x3000, size=0x1000)

[============================ ] 96% (128/133 pages)write(addr=0x20005000,size=0x140)
writeBuffer(scr_addr=0x20005000, dst_addr=0x4000, size=0x140)

[==============================] 100% (133/133 pages)
done in 0.060 seconds

Verify 8508 bytes of flash with checksum.
checksumBuffer(start_addr=0x2000, size=0x1000) = 917e
checksumBuffer(start_addr=0x3000, size=0x1000) = 9f85
checksumBuffer(start_addr=0x4000, size=0x13c) = 67f9
Verify successful
done in 0.013 seconds
CPU reset.
readWord(addr=0)=0x20007ffc
readWord(addr=0xe000ed00)=0x410cc601
readWord(addr=0x41002018)=0x10010305
writeWord(addr=0xe000ed0c,value=0x5fa0004)
```

But uploading the same sketch via programmer (again atmel sam-ice):

```
Open On-Chip Debugger 0.9.0-gd4b7679 (2015-06-10-22:24)
Licensed under GNU GPL v2
For bug reports, read
http://openocd.org/doc/doxygen/bugs.html
debug_level: 2
Info : only one transport option; autoselect 'swd'
adapter speed: 500 kHz
adapter_nsrst_delay: 100
cortex_m reset_config sysresetreq
Info : CMSIS-DAP: SWD Supported
Info : CMSIS-DAP: JTAG Supported
Info : CMSIS-DAP: Interface Initialised (SWD)
Info : CMSIS-DAP: FW Version = 01.21.0076
Info : SWCLK/TCK = 1 SWDIO/TMS = 1 TDI = 1 TDO = 1 nTRST = 0 nRESET = 1
Info : CMSIS-DAP: Interface ready
Info : clock speed 500 kHz
Info : SWD IDCODE 0x0bc11477
Info : at91samd21g18.cpu: hardware has 4 breakpoints, 2 watchpoints
target state: halted
target halted due to debug-request, current mode: Thread
xPSR: 0x41000000 pc: 0x000005e8 msp: 0x20007ffc
** Programming Started **
auto erase enabled
Info : SAMD MCU: SAMD21G18A (256KB Flash, 32KB RAM)
wrote 32768 bytes from file C:\Users\\AppData\Local\Temp\buildbb61b02d674ae2bfb0845dfb247346a1.tmp/Blink.ino.elf in 3.812762s (8.393 KiB/s)
** Programming Finished **
** Verify Started **
verified 16700 bytes in 1.427786s (11.422 KiB/s)
** Verified OK **
** Resetting Target **
shutdown command invoked
```

Seems to work because no error is shown. But Arduino is not executing blink sketch and is not accepting any new sketch via USB (even with double-tap-reset). I have to flash the bootloader again (with sam-ice) to get the arduino back into a working state (to accept sketch upload via USB)

What's wrong? Any hints?

br,
Alex