Help getting java files working after ROM update

[chaosbuzz]

I use a medical software suite called Uptodate on my windows mobile device very frequently at work. On the stock sprint rom, this program worked, and I believe it also worked on mightyrom 4 and the supermedia rom (both win 6.1), but did not work on the EnergyRom or 6.5 roms I tried. I recently flashed with the awesome silence 6.1 rom and while the program starts, it doesn't display the content in these jar files (just a blank screen) when I try to pull up articles (it did this with the 6.5 roms too). I tried installing .net 2.0 and configuing the program to use it and that didn't help. Have any of you had trouble running java based programs on ROMS and what did you do to fix it. Any help would be hugely appreciated, I have been trying to figure this out for some time. Thanks!