Problems with Sony DW-D56A

I recently flashed my drive with newer firmware. I was having problems with DVD playback skipping around. The new firmware fixed that problem, but now whenever I start an application that does a cd check, that program crashes back to desktop. I tried other versions of the firmware , including the Liteon versions with the same result. I flashed back to the stock version, and the application works fine. I’m not sure what the problem is. Does the new firmware mess up the cd check? Would reinstalling the program with the new firmware fix it? This is a long process, and I wanted to check here before I wasted my time with a dozen reinstalls, reflashes and rebooots.