Some games suffer this issue if both boxes are not running the game from the same media. For instance:
The game Timesplitters 2, while attempting to system link can lose connection if xbox A is running the game from disc and xbox B is running the game from the hard drive. The player running the game from the disc typically gets kicked immediately after a system link match starts. I believe this is due to xbox B loading the game faster (from the HD) than xbox A.
I dunno if this is your problem but this is the first idea that popped into my head for some reason.