what exactly do you mean with:
... but we kept going in unsynced!
You mean you are playing and after a while you get an out of sync error message?
But if you get checksum errors after loading, everything is ok! You simply have different binaries and/or data in this case!
To be shure the data is checked, this should be set in glest.ini:
NetworkConsistencyChecks=true
If this is set on both ( server and client ) and the game starts successfully, you should not get out of sync ( with 3.3.4 megaglest )!