Hi Agisoft,
I've noticed in 1.6.3 that when I edit a particular NAD83(2011) UTM XX projected coordinate system to make a compound coordinate system in NAVD88 height that it overwrites other projected coordinate systems I've made. For example if I start with the NAD83(2011) UTM Zone 10 North PCS and edit it to add NAVD88 height as a compound coordinate system, then when I try to add one for NAD83(2011) UTM Zone 18 North, it overwrites the NAD83 Zone 10 north one (or at least it looks like it does in the available CS menu). I've seen this with NAD83(2011) in UTM 10, 17, and 18.
Typically I am choosing to edit in the dropdown as I am creating a DEM/Ortho, although some times when I am exporting. My standard practice to to process with geoid heights in the appropriate GCS (NAD83(flavor) or WGS(flavor)). If I'm doing something wrong, sorry for the erroneous bug report.
Andy