AGS standart inventory window aligns items to top-left. Thus, if your item sprites are smaller than item size parameters set for inventory window, then they will appear "shifted" up-left. The only workaround I know is to make all items have same size by adding transparent boundaries where needed.
So, what about making inventory window automatically align items to the centre of each corresponding item box? Or, perhaps, add an "alignment" property to the inventory gui.
Sounds like a reasonable request to me.
I second this, even though I make sure all my inventory icons are the same dimensions. This would still be useful.
Thirded.