I just updated my iPhone from version 2.1 to 2.2, and I had a LOT of my apps put into categories, and when I updated them, they were no longer there. I'm guessing that categories modded my files or something inside the phone so that they're all turned off on the main springboard page? Is there any way I can turn them back on? I don't have access to Cydia, Settings, or the Categories app.
I have the exact same problem, and I can't see a way to install any new Cydia apps, since Cydia itself is one of the hidden apps that was previously 'filed' by Categories.
I tried uninstalling and re-installing all of my apps, in case that 'reset' the show/hide setting, but that didn't work.
OK, nevermind ... hunted around some more. For anyone else who may stumble across this same problem, the answer is here: