I've had problems with lateral weirs in the past. I had multiple lateral weirs in a channel and several different sections where the flow input changed. If/when the flow input changed the downstream weirs went nuts with negative flows and the like. I sent my model to the Corps of Engineers as a bug and they confirmed that it was.
here is a link to the thread I posted
http://www.bossintl.com/forums/showthread.php?t=14239