Hi dsm iv tr,
I had a simular problem on a 7 speed and checked my F&R deraileur adjustment and alignment several times. A friend told me to change the chain and problem solved. After inspecting the chain it wasn't stretched very much but it had quite a sag from side to side. In the end I think the chain was whipping sideways as I shifted.
I would still find it odd that your trouble started after you did the BB.
Good luck!