DLTimmons, I duplicated what you are seeing. Until the firmware is fixed, there is a workaround.
1. Do a CTAXCFG and set the Initialize Output Position = 0
2. Do a CTAXTRAP and set the Target Position = 0
These two steps will do absolutely nothing except complete without error.
Then proceed to do your normal CTAXCFG with your normal Initialize Output Position value, and your normal CTAXTRAP with your normal Target Position value.
This workaround will continue to work even after the up-and-coming fixed firmware is loaded.
Let me know if you have any more problems, or if this doesn't work for you.