Now that you mentioned about folder location. It maybe related to the folder depth.
Those missing file attachments all seems to be two folders deep.
e.g. images/Apprentice/AttackPose2/Arm_LR.png WHERE the spine folder path is set to "images".
Those attachments are very small. All parts are just around 200x200.
The editor and preview panel is displaying everything fine only exported GIF and MOV has this issue.
BTW, turning off "limited scanning" do really fix the issue.
I think its better auto turn it off when exporting.
Thanks