Yup, I've also seen problems with a larger favorite list. We have one for just normal surfing. Over time more channels got added. Then the last couple of weeks, some mentioned that YTV is on. So I put it on.. then noticed that all my Joeys showed Amazon Prime in their guides, but nothing I could do would put it on the favorites list on the Hopper; it showed the list in the interface but nothing in the guide. No error, just the same.
So I thought that, yes, it might be a hard-coded (dumb for these days of programming) linked list that has a fixed amount of slots. So while Amazon Prime was supposedly not on the list, but I definitely added it; I deleted just one ESPN slot and then called up the guide, and there is Amazon Prime, sure as heck.
Confirmed, Favorite lists have a fixed maximum size.