Well I seem to of royally cocked up the Ras PI method every time I use this hex file for flashing https://dl.dropboxusercontent.com/u/143860/BitForce_SC.mrrad.hex the process shows the following

Flash on AT32UC3A1256
Size(detected): 262144
Pages: 512
Page size: 128 words
burning...
addr: 0x8003FE00 page: 511
verifying...
addr: 0x8003FE00 page: 511
511 bytes total
Done.

I then run the following commands

jtag> instruction HALT
jtag> shift ir
jtag> dr 0
jtag> shift dr
jtag> shift dr


this should then start the front LED Flashing but nothing happens.

and CG miner says it is unable to start the device

Any ideas?

edit: I do not know how to compile firmware with atmel studio

edit 2: i found with the LED's on the back that are on are the one next to the power power connector and also if i remember correctly the  1st LED on the left (i belive these are the active chips LED's) this may help some one diagnose my issue