it's not the jailbreak, the jailbreak is fine
but
the developers of cydia apps get the jailbreak the same time the users do, so they still have to get their apps/mods/add on's compatible
a sure way to avoid issues, don't go installing hectic sprinboard/mobile substrate extensions right away (these include iblacklist, sbsettings, winterboard, yourtube, safari download manager, 3gunrestrictor) all the lovely "we are convincing the OS it's doing something else" mods, because the OS isn't quite what you think it is anymore... c'mon guys, surely this makes sense to more than just me?