Hello Clay. I had/have a somewhat similar problem. Though I bought my PRT alpha used.
I can resurface the table, then install a V-bit, and zero it at any point of the table, and move the bit around the table, and find that the tip of the bit does not remain the same distance from the table top...…. I posted on this a long time ago, and talked to tech support. I got all kinds of helpful suggestions from the forum, and tried out everything anyone could come up with. Someone suggested finally that my Z bushing may be worn, and upon removal, it was in fact worn.
And I started to re-align my Z axis after putting in the new Z bushing (I replaced all bushings while I was at it). But I never got back to it because I got caught up in making a big 3D model, that turned out to have big problems...… so I am not firing on any cylinders, so to speak.
Maybe by parking my machine, I am leaving it where I HOPE it will finally work after I finish the re-alignment.... better false hope than no hope....
Sorry to be of no help, other than to point out odd things like what you have going on, may not be easy to fix.
Good luck, and unlike me, press on! Chuck