Does anyone know what the effect of having the desuperheater on has on supply/return temperature differences?

I'm seeing about 14*F increase between return and supply (at vents in room) when running (I believe Stage 1) on a 5-ton climatemaster. (approx 70in, 84 out) with the desuperheater on.
should the supply temp increase more if the desuperheater were off?

Climatemaster makes a point to test with the desuperheater off when comparing to their published tables, so I assume the difference could be substantial?

No.

Desuper should make only about a 10% difference, less during long runtimes as the water flowing through the desuper warms up. That said, go ahead and test with it off to eliminate this issue

14 degree temp change is low - 20-25 is desirable.

At this point I'm betting you have a heat loss or leakage problem within your supply or return ductwork. Try measuring return air temperature at the air filter or other place as close as possible to the unit itself. Just a few CFM of cold air from an unheated area getting into the return will dramatically cut return and supply air.