I have had a similar problem concerning cydia.I have a the 3GS that just been unlocked and jailbroken to bb 6.15.00 and version 4.2.1(8C148).Everything looks as it should and I can use cydia as per usual only thing is my 3rd party apps/games/themes that Iv downloaded that used to work when I dragged/dropped in itunes ,now dont work.Also some themes/games Iv got though cydia dont show up or work so is there anything else I need install to make my iphone verify/launch 3rd party apps etc.
You said some not all so only some don't work right? You might want to check if they are compatible with 4.2.1. What are some examples you are trying to use that dont work?
basically all of my 3rd party apps/games that downloaded are sitting in my itunes library and when In try and sync as per usual I get an error msg saying that the items could not be loaded ,strange that though because a week ago I had verion 3.1.3 bb 5.14.02 and it was jailbroken but NOT unlocked and the apps/games worked fine,Iv had it unlocked and now with the bb upgrade and new version everything looks as it did and I can access Cydia but I tried getting a theme and one game from Cydia to chk if its my handset but winterboard couldnt launch the theme and quake 3 is showing but doesnt load up..
Well some themes aren't compatible with 4.2.1 so like I said you should check compatibility. Usually if it doesn't say it's compatible it isn't.
As for apps or games, if they're in your iTunes from before and wont sync to your phone, I can only assume you're talking about cracked apps which we don't condone or offer help with.
If that's not the case then you might want to restore and rejb to see if the problem resolves. That's the best advice I can give you.