I have gone through a new path testing our custom board with SAMBA and comparing the result with the develoment kit.
When SAM-BA try to program the MCk register Jlink issues the following error: Write Memory error @ address 0xFFFFFC30 word access: Adpative clocking timeout. I suspect that the CPU just dyes because when I use gdd in standalone mode or via Eclipse it works (not 100% but it runs).
This is the trace of JLink for our board:
SEGGER J-Link V4.46f DLL Log
DLL Compiled: May 10 2012 08:30:05
Logging started @ 2013-02-04 19:22
T21EC 000:388 JLINK_Halt()
T21EC 002:311 JLINK_WriteReg(CPSR, 0x000000D3) returns 0x00
T21EC 002:371 JLINK_ReadMem (0xFFFFF240, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 002:984 JLINK_ReadMem (0xFFFFEE40, 0x0004 Bytes, ...) - Data: A2 05 9B 81
T21EC 003:164 JLINK_WriteMem(0xFFFFFD44, 0x0004 Bytes, ...) - Data: 00 80 00 00
T21EC 003:382 JLINK_WriteMem(0xFFFFFD00, 0x0004 Bytes, ...) - Data: 05 00 00 A5
T21EC 003:604 JLINK_Halt()
T21EC 003:621 JLINK_WriteMem(0xFFFFFD44, 0x0004 Bytes, ...) - Data: 00 80 00 00
T21EC 003:831 JLINK_WriteMem(0xFFFFFC30, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 004:041 JLINK_WriteMem(0xFFFFFC20, 0x0004 Bytes, ...) - Data: 02 00 00 00
T21EC 004:252 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 004:427 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 004:602 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 004:777 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 004:951 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 005:126 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 005:300 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 005:476 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 005:652 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 005:827 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 006:002 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 006:178 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 006:352 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 006:528 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 006:705 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 006:878 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 007:053 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 007:227 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 007:401 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 007:577 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 007:752 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 007:926 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 008:100 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 008:275 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 008:449 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 008:624 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 008:800 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 008:974 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 009:149 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 009:323 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 009:497 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 009:672 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 009:848 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 010:022 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 010:197 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 010:371 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 010:544 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 010:720 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 010:896 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 011:070 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 011:245 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 011:419 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 011:593 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 011:768 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 011:943 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 012:118 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 012:292 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 012:466 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 012:640 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 012:815 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 012:990 JLINK_ReadMem (0xFFFFFC24, 0x0004 Bytes, ...) - Data: 00 00 00 00
T21EC 013:164 JLINK_WriteMem(0xFFFFFC20, 0x0004 Bytes, ...) - Data: 01 FF 00 00
T21EC 013:373 JLINK_ReadMem (0xFFFFFC68, 0x0004 Bytes, ...) - Data: 09 00 00 00
T21EC 013:547 JLINK_WriteMem(0xFFFFFC30, 0x0004 Bytes, ...) - Data: 01 00 00 00