Bummer
Just to make sure I understand you correctly: the apps are downloading / installing themselves while you're on wifi and plugged in. ( not while syncing itunes )
If that's the case, likely something IS behaving funky.
( but note I'm not running iOS 5 so there might be somewhere else you need to change things that I'm not aware of...)
You might try the following
1. You can try the old 'wake up the prefs' trick: basically you change, then rechange your settings. in your case check the boxes ) close settings (maybe even hard restart your iphone ) then uncheck them again
2. If that doesnt work you might try to Reset your phone (Settings > General > Reset) starting with the least destructive first . (naturally back up first)
Last resort, If you really dont want the apps for any current devices, you can delete from iTunes - then drag a copy from the trash as backup (YMMV It works on Mac OS 10.6x / iTunes 5) Of course that's not a longterm solution
Good luck if all else fails go thru Apple's 5 R's ( which eventually walks you thru a full install )