I'm tracing some disappearing skills that I though I had fixed in OS-397, but it seems the problem is actually lying in the code. The call count("SKILLSIT","NONDEFAULT") does not seem to actually include the situations, and after some exploring, I find that count("SKILLSIT") doesn't either.
I've traced this to SkillDisplay.getSkillListInOutputOrder() which is called from JepCountSkillSit.count() via base class JepCountType().processCount. Form there we go down to pc.getDisplay().getPartialSkillList(), and that result does not include the situation skills. CharacterDisplay.getPartialSkillList() retrieves the list from the SkillFacet, where I've lost the trail...
The result is that the count does not include the situation skills, but the are returned when iterating over the skills. and so the list is truncated in the end with one skill missing for each situation skill listed earlier.