Inverted z and limit switch software problem?

I'm finding my Series-2 D840 stepcraft profile lacking in so many ways, and also very buggy... I would love to switch over to the non stepcraft tampered UCCNC but I dont know why it wont Jog.. is there any way to fix that?

my typical problems in the stepcraft Uccnc profile are as follows...
1) often the software wont let me reset because it thinks the limit switches y-,x-, and z- are triggered... (which they arent and eachc time i even unplug them and replug them in to make sure there isnt a shortage.
2) my z axis likes to home in the wrong direction, heading right for a suidical plunge towards the machine bed..

I contacted stepcraft about this, and no answeres or help. So as a friend of mine suggested, turn to the forums!

These problems arent consistent, they happen maybe once out of every 4 or 5 times that I run the machine. which is often enough to make it almost not worth using the machine because ill spend a few hours trouble shooting only to have zero luck and somehow magically the next day it decides to behave...

Any ideas?

Thanks,
John