Work offset issue; cutting air on the z

I created a part in Alibre and imported it to Sprutcam, ran the tools, just a couple of endmills and a few holes, all went well. However, I took it out my Tormach, running Mach3 (upgrading to Pathpilot next week), and uploaded it, ran it without tools to be sure nothing would bust. It looked a little high on the Z. So I tooled it up, knowing the outcome, and ran it through its paces, and sure enough, it is off about 2 1/8 inches high on the Z, and I cannot for the life of me figure it out. There appears to be some additional offset in Mach3 that is adding this, so I zeroed it out, and not having a lot experience messing with Mach3 as it's pretty reliable, I tell it what to do and it just does it. This time is odd. Any ideas? I'd be mighty grateful.

Thank you.

I did zero on the part without tooling, input tooling measurements, and even set off the tooling. Still, 2 inches above the workpiece.

Where is g54 or whatever offset your using set at on part in Sprutcam
It needs to be in a place you can locate, like top of material or vise.
Picture below shows g58 set to center top of material.
Attachment 394942
This is for Sprutcam only. Mach tool table and offsets also have to be set correctly to use the offset in CAM correctly.