Made a brainzip from the Windows machine. Deleted the brain on the Macbook Air and from webbrain.
Synced with webbrain again from Windows machine.
Restored the brainzip onto the Macbook Air. (All statistics matched at this point)
Synced the Macbook Air with webbrain. (Now internal file attachments does not match again, even farther off than originally in above post.
Ran "Check for modified attachments" and now internal file attachments is closer to the Windows machine but still way off.
Have version 188.8.131.52-b of TheBrain on both machines.