There are no default values or anything its super confusing it seems to happen to only the boxes that are lookup fields the choice boxes don't seem to have an issue.
The save button is just submitform(formname) and then shows the please wait with a context variable.
I have 4 other forms in my app and none of them seem to have this issue.
Also the form works normally in edit mode, but i do see it glitch out for a seconds and remove the selected items for a split second before saving.
Edit: There seems to be an issue with the Field disambiguation it isnt loading properly.
I attempted to recreate the form with a container and it will not grab any of the lookup fields with the tablename[@fieldname] format.