The OP was trying to detach them from the Android market (as in showing up) not update them. In TiBu there's an option to "break" the link, but for him, the links are not staying broken. I have the same issue with SwiftKey, but just live with it...
Every Market/App store ie. Getjar, Amazon, and Android (plus a few others) is in most cases the only route to update an app purchased/downloaded from that site. The problem is, when an app has an update in line for it, it shows up in the Android Market even though that's not where the app came from. It just gets annoying after awhile especially if you have a ton of Apps and the top of the My Apps page in the market is filled with Apps you can't do anything about THROUGH the market. As a side note, not all Apps are the same version so can sometimes stay in an "update" state because of that. (Amazon is usually always a little behind in versions. A good example is ES file manager)
