Exactly. What I know it is like that: for instance you got 3d model of your character in your 3d application. Let say that you downscaled your model in Z Axis 50 % so for 3d application your model scale is ( (X 100%, Y 100%, Z 100% + downscale modifier Z -50%) = X 100% Y 100% Z 50%). But most of the exporters for game engines doesn't see your modifier, therefore your model in game can be out of scale. X Form merges your modifiers with your model. So your 3d application after X Form will see scale (X 100%, Y 100%, Z 100%) but size of your model will be the same as before X Form. So everybody is happy and exporter will export your model with correct scale.
This can be solution for your problem. If not, keep in mind for futre this tip. It helps you to avoid many bugs.
Sorry for my english, It's not my native.