Not sure as I don't know the game well, hell I don't even own Factions yet, but I have a few ideas of what it may be.
If factions is more graphics / ram / CPU intensive than the original, it could potentially cause problems. Improper coding / lack of time spent coding could result in random "bugs", "glitches", and an over all "laggy" feel. If as the game is out longer these issues dissapate, then you can fairly safely assume this was the issue. Also, if Factions uses multiple ports for its internet connectivity you may want to make sure that said ports are open in your modem / router.
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