My guess would be that you are either getting too strong an i/r signal into the Tivo or that other emitters are reflecting back into the Tivo (assuming there are emitters on the gear). Another posibility might be that the Tivo got a firmware upgrade down the cable that you are not aware of that affected the units ability to be controlled by a learning remote. We had this problem about 2 years ago with our Foxtel here in Oz. The boxes got a firmware upgrade and all of a sudden everyone controlling the boxes with learning remotes or control systems like crestron had problems with scrolling functions.
I guarantee I'll tell you the truth and I guarantee I'll tell you what you need to know but I can't guarantee that I'll be telling you anything you want to hear.