Wow man thanks!!! We really appreciate you putting your faith in this ROM and we LOVE hearing how well it's working for you. We have some more tricks up our sleeves and gbhil has been acting as an open book of knowledge for us to pick his brain so I'm sure you'll see more cool stuff in the future.
Nick is correct in that it's not a bug with the ROM. This has to do with how titanium is being used. For the example of flashing 2.4 over 2.3 in which you only wiped cache and Dalvik, there is no need at all to use titanium. Only the factory wipe clears your home screen, not dalvik or cache.
What happened was, you probably wiped dalvik and cache and flashed 2.4. None of your icons or anything were touched and you should have been fine (because you didnt do a factory wipe) but then you probably did a titanium restore? Guess what that did ..... double icons/widgets
You only need titanium when doing a full wipe or just a factory wipe. Not necessary when doing a cache wipe or dalvik wipe. If you want to check it out for yourself, just go into recovery and do a cache wipe and dalvik wipe then reboot. Your phone will be absolutely fine and all your icons and widgets will be in place.
Hope that helps.