I finally got my problem fixed. See the thread
http://www.eq2interface.com/forums/s...ad.php?t=10998 for a lot of info about what I had tried (and none of that worked).
What did work? Well, I loaded up a character on another computer that doesn't have any mods on it at all, just bare bones EQ2 install. I had no problem saving the bank bags. I then took my char's UI file and copied it to my normal computer. The bags still worked. Because it was SOE's default UI file, I had to do a bunch of moving stuff around so that it looks just like Profit's default 1280x1024 again, but now everything works just fine. I've since even moved and resized all bags just to make sure it would continue to work, and it does.
So, I have a good working file, still using Profit, looks just like what I had pre-GU45 (with additional bank slots however), but had to use SOE's default UIsettings file, not the ones GM9 provides for ProfitUI. No clue where the issue lie, but that fixed my problem with bank slots.