Why not call 214-585-0444 or email Support@adventure pilot .com and get the answer from the people who made the device?
This is what I learned:
Ind. Alt is what your airplane's transponder's altitude encoder is telling ATC your altitude is. Right or wrong, that's what they're seeing.
Alt.(GPS) is your altitude derived from the GPS signals you're receiving. Great to avoid "controlled flight into terrain".
Alt (agl) may be coming from data used in producing charts? Don't know that answer but I still use it.
The fact that the three readings do not agree with one another is immaterial; it's just the way it is. When informing ATC of my altitude I say Ind. Alt to eliminate any discussion, but I also keep an eye out for the other two display readings just for safety's sake.