However, if you don't skip promoting the unit for a number of levels, does it give the same problem?
It looks exactly like this: I qualified up couple of units (at level 11) and then have not promoted them for a while (earned 50-100XP above). And then selection of any promotion skipped any gained quality up promotions.
Here is save: https://mega.co.nz/#!ZF4kXISD!5I5oXTuhG-7-9BY6cftTHhd6v_5mz2ki_PZUgPvt3Yw
Just try to promote Drake (Privateer).
P.S. No such problem if unit promotes every level.
is there an upgrade taking place in there somewhere?
I thought about it for a moment, and then realized that my hero units were affected as well. So, repro scenario should be simple as I described.