I don't think this is the same problem. We are not syncing our library to the iPad, we are sharing it, and therefore there is no sync and there is no option to check or uncheck songs.
I am suffering from the same problem described in the OP. The really irritating bit is that I have been using homesharing on the iPad for over a year with no problems. Since updating to iOS5 on release day, tv show sharing has been broken. As described above, multiple instances of the same show/season (upwards of 5 duplicates) Each instance works in it's own right as a link to those episodes. More importantly, only some of my TV Shows are showing. In my case, it only gets to the very first shows in 'B'.
I have been using Homesharing for a long time, on iPad, iPhone, iTV(1) and for all the various members of my family on their respective computers. In most of these situations it still works fine. Even on the iPhone on iOS5 it works as well (possibly even better) as it ever did. This problem is isolated to the iPad, and I would guess, large librarys.
Come on Apple, Fix it! In most other respects a great update, but the removal of multitouch gestures, and breaking homeshare are a huge step backwards for the iPad.