Bill,
I'm not at my shop right now so it's hard for me to test those settings but, I have a couple of thoughts... the first thing you mention is that you just rebuilt to increase table size.... what is happening with your linear motion devices (Bearings, wheels, etc.) Is there perhaps something binding somewhere? Seems like you should have have enough voltage to run things without missing but just for giggles why not try changing your steps per min to see if that stops the missing step problem?
HTH,
Sid