I haven't tried cm9 alpha 2 but in reality unless the ramdisk has changed then there is no logical reason it shouldn't work. The only difference between the cm9 and the stock kernel's is the ramdisk.
If you wouldn't mind so we have a common frame of reference can you follow these steps and report your results.
1) Please make sure your doing a full wipe before flashing either ROM. I religiously use HB's Wipe tool..... that way there's no question that the system is clean.
For Stock:
2) Flash Any stock based ROM. I.E. Ultrabase (1.5 Preferably), Greeza's or a straight stock ICS ROM.
3) Then flash the kernel. No need to boot into the ROM first, before flashing the kernel.
For CM9:
2) Flash CM9 (i will test alpha2 and see if there is any reason for a problem ASAP).
3) Flash Gapps.
4) Flash Kernel.
A couple of things to keep in mind (and part of this i can help with. Shocker here but i have no clue how md5sums work... I've never used em), you could simply have a bad download, or a bad flash.
I'm currently running UB1.5, I'm downloading cm9 alpha2 at the moment, but alpha 1 seems to work with no issues.
Two side notes:
1) What bootloader version are you on - Again this shouldn't matter however it is good information to have.
2) Can you provide a logcat when the system is boot looping.
Note: I did get boot loops in the beginning, but only if I flashed the opposite kernel.



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