Thanks I'm glad you like them :)
I also have 4 T65 Xwings (2 Core (from about 6-8 months apart), Booster and the Transport pack) and they seem to fit OK for me and they are all the same size. I'm not sure what to suggest, I'll double check the files to make sure I've not accidentally made it smaller when I last updated it.
Since the xwings all fit differently either the boxes are different sizes, which suggests irregularities in the printing, or the xwings are different sizes, which seems unlikely due the manufacturing process.
Very strange! you could measure the ships and boxes to make sure they at least are all the same size? Keep me posted.