I have bagnon for classic running on 7 different toons (on 2 separate accounts) and until this evening, there hasn't been an issue. Then one of my chars received a 10 slot bag as a quest reward'Gunnysack of the Night Watch'. I placed it in one of my bag slots and a little later I noticed that one bag didn't appear on the screen. I have worked it out that it is the middle slot that disappears. It doesn't matter what bag I place in the middle slot (8 slot woollen, Gunnysack, arrow quiver) the contents of that bag vanish from the screen.
I have tried turning bagnon display options off and on, resizing, changing scale, order etc, but nothing makes the middle slot appear.
Will do some further testing (disabling other addons, trying different bags etc) and add results onto here.

Just decided to delete the bagnon.lua from my savedvariables folder and it then worked, so closed the issue. I'm sure you already have enough to work on.