Spoke to Larson and he mentioned this is happening on his laptop. I researched it for him and this issue is due to having the same Steam account synced over multiple devices. After updates or the like, what is done on one device may not be carried over to others of which you are using the same account. I have also seen this issue after Steam updates on my main PC that I use. Nothing to be done about this except re-adding the favorites as this is a Steam issue they haven't really addressed.
Vicari 1st MRB's post in Resolved - Server Favorites Not Showing Up was marked as the answer