Yeah that's a very likely explanation for the problem.
What I like to do is place my unsynced modules over slightly on the edge/off the map in my missions so I can easily see them even when zoomed out. Your test mission had them jam packed in the corner and all overlapping each other so when zoomed out, I thought you only had one module there. Lol. Probably easy to lose track that way.
Hopefully the duplicate data modules thing is the culprit.