Im not sure if this is caused by your mod.
On some Items i have a NBT tag so i cant stack them. For example i got 20 bukets fill one with water and throw the water away and now i cant stack them anymore becouse something change with the NBT Tags.

This happens with a lot of items not every time but often.
jjust like i said im not sure if this is Itemphysics related but as far as i know its the only mod which changes items. This happens to Vanilla and Mod Items. Newest Version for 1.12

This is not an issue of ItemPhysic, not sure why it's caused. Maybe try it out with only vanilla minecraft.