Also, have a look on the Omnia II forums. Some people there have had similar problems.
I forgot to mention that as well as organizing my start menu into folders, I used MemMaid to arrange the start up programs, making sure that the AutoKeyLock.lnk is last and poutlook.lnk is first. I had read that somewhere and have tried it. Like Ì said, I don't know what specific thing helped, but after having had the problem on this phone for a long time, I have now had NO slowdowns for over a month.
I also formatted my memory card using my PC, so it's possible that might have helped as well. I did try that before and it didn't help, so I didn't think it was worth mentioning, but as someone else did it and it seemed to help them, it's worth trying it.
If you want to try the start menu idea. I used Resco File explorer to move the icons in my Start Menu folder into folders for different categories (accessories, media, internet, office, navigation and system tools) which keeps the first page of the start menu relatively small. I also do it for my convenience as it helps me navigate the phone easier.
If none of this works get back to me. There must be something I've done to make the problem go away because it doesn't happen to me anymore. It could be something really simple that I've forgotten about.
Hope this helps.