Probably worth to compile your server with serversavegameversion bumped to 112007?
It is compiled with standard trunk simversion.h, which sets savegame version to 112007 iirc...
Fifty, which OS are you using? Maybe I could set up some debug servers and compile executables for you to find revisions which do (not) work.
One idea I had: maybe the new code to allow more than one station per tile is not network safe in some regard?
Edit: Fifty, could you try the following: write 'threads = 1' into simuconf.tab in My Documents/simutrans or ~/simutrans. This will disable the multi-threading for you. If it does not work, then I will restart the server single-threaded to test again.