When you delete them from your phone they aren't really deleted from iTunes. PITA, I know. What I've done is use the main apps list in iTunes and right click on the app and select delete from there.Mine is in iTunes. You know when you hook your phone up? Go to the apps tab. It'll show me tons of updates - a very good amount of apps that I deleted via my phone. I'd love to fix this if someone can tell me how.
When you delete them from your phone they aren't really deleted from iTunes. PITA, I know. What I've done is use the main apps list in iTunes and right click on the app and select delete from there.
Strange how it will delete from your phone, sync & all but not actually remove it from iTunes.