Michael, I have had this programmer since they first came out and had it updated last month I think.
The behavior I described is only happening with the 5995. I have tried a 5945 and a 5955 both work correctly. The servo responds to the knob but not the buttons. Same in auto when you can normally get them to sweep.
If I reset the servo then it works but goes back to 180 throws. However I was advised to limit the throws so as not to reduce resolution.
I have checked my programming on another servo and it seems fine.
If you push the buttons it will not go to 900 or 2100 put another servo on it and bam it goes there and center no problems.
My LHS ordered it by mistake, maybe I should see about changing it although he normally will not do it.

The servo works fine when connected to a radio system