This is a game bug that even affects the Default UI. I had some bank bags that refused to remember their settings so here's what I did.
Loaded up the (server)_(character name)_eq2_uisettings.xml
file in my EQ2 directory and removed all the lines that looked like:
<Window Name="Bag_clone_0_-3" alignment="0" alignment_offset="214,-4" size="154,374">
<Properties bag_size="36" clone_version="4" icon_padding="0" icon_size="35" version="1" />
I did notice two of these Bag_clone
entries had no Properties tag which was probably the two bags I was having problems with.
Saved the file after I made a back-up copy. This did cause all my bags to revert to default settings and placement; however, I was able to get all my bags where I wanted them. Apparently there's a limit somewhere, especially after changing to different sized bags as it seems to keep the old bag's settings. I found entries for 12-slot bags that I hadn't used in months.
Hope it helps.