You might want to try deleting your preset preferences first from your P6 folder, not as hard as it sounds there is instructions on CL's web site for doing this. Preferences when corrupted can have strange effects.

If you haven't done much in the way of reorganizing your P6 runtimes and such then a clean install might work, make sure you uninstall "everything" first [important]. You can back up the runtime if you like, that won't afect anything and then put it back after the reinstall. 

Also I never went straight from base to SR2, I had installed SR1 first. I know SR2 is supposed to have elements of SR1 in it but maybe not all, just a thought!

Put SR1 in first and then run SR2, you never know, it can be a strange beast at times.

Just for your info, if you do get it to run, it is a far more stable piece of kit after SR2, still one or two niggles but I can live with them!

Good luck!

Injustice will be avenged.
Cofiwch Dryweryn.