Oh god... experiencing problem after flash:
[2013-07-04 12:31:24] Started cgminer 3.3.1
[2013-07-04 12:31:27] BitForceSC detect (2:3) 2nd init failed (0:-7) - retrying
[2013-07-04 12:31:28] BitForceSC detect (2:3) init failed 3 times 3.31s
[2013-07-04 12:31:28] BitForceSC detect (2:3) error identify reply (0:-7)
[2013-07-04 12:31:28] Disabling extra threads due to dynamic mode.
:[
The red light is flashing on/off 2-3 times a second. When I hook up JTAG (AVR DRAGON) it flashed quietly like normal and I can still re-program it.
I flashed with the untouched firmware 1.2.5. Anyone know whats wrong? :/
EDIT: Alright, after very quick trial and error, this has to do with the "#define __ASIC_FREQUENCY_ACTUAL_INDEX 7".
Apparently 7 doesn't work on mine. I got 5 working fine, will try and adjust with 6-8-9

I have the same problem with my Jalapeno.
and got this problem.
Reflashed with __ASIC_FREQUENCY_ACTUAL_INDEX 5 - same problem again...
with __ASIC_FREQUENCY_ACTUAL_INDEX 1 - same problem.
Also after upgrade there is only one big LED4 blinking and LED1 (power), but before upgrade there 2 LEDs on the other side of board was on too...