After more tedious trial and error, I've decided the problem described above was caused by some sort of ccf import bug. Originally I had imported my 2000 ccf into the 3000 using the import tool. The imported devices were causing the Tivo hard button code corruption. It has nothing to do with the multi-Tivo device codes or hardware issues, fortunately. Now that I've created a new pcf from scratch and re-learned the IR codes, there have been no problems with the hard buttons.