Did you get this worked out? If not, the best place to post is on the War in the East forum at matrixgames. I'm not sure what could be causing your problem, but you are more likely to have someone answer your question that has experienced something similar (or could advise you on how to avoid it).

There was a bug in comparing your username for the purposes of determining whose turn it was. It had to do with case sensitivity. You could be signed into multiplayer with a different username from an upper/lower case point of view than your slitherine account name. We've fixed this bug in the 1.02 ...

Did you create this game yourself, or did the other player create it? We had a known problem that if a game was created while the PBEM box was checked, then it would think it was a PBEM game and not save to the server. This has been fixed in the beta patch. If you created the game and are sure you d...