When I hooked up my limit switches, I had to invert the limit logic in the Galil card. I like to have current flowing through the switches until such time as they become activated by table overrun. The Galil default is just the opposite..I think they call it "active High", but there is a 50% chance that its the other way.
Anyways, the command to do this inversion in galil-speak is CN -1. I put this in the Camsoft startup.fil as:
COMMAND CN -1
Whether this is what you need, I don't really know. I assume you've got them hooked up correctly. Of course, you must also write logic to turn on the appropiate limit light when the input is triggered.
What kind of gearing are you running your rotary axis through? How many counts does this stepper require per revolution of its own shaft? Are you saying you cannot alter the number entered, or it does a conversion for you?