I've had a few reports like this, but have been unable to figure out what is going wrong.
You can try the 1.0 beta version of LTN-T. By now it is pretty stable and most of the code has been rewritten. Hopefully that also fixed these multiplayer issues.
I run the server on a qnap on the first start I also had the error message. The mod files copied from the server to my mod folder was the error gone. my teammates were able to make direct connections via the server synconization. In your case try to share the mod data after start the map . these are in the factorio / mod folder or you use steam in (C:)users/"your user name"/appdata/ Roaming/ factorio / mod
I hope it helps