This seems to due to a change in cr_skills.lst where the skill detail has been changed e.g.
Acrobatics KEYSTATEX ACHECK:YES TYPEexterity.ACHECK.Base
The change to TYPE causes the behaviour.
If I change the TYPE to Dexterity.Base then the skill is removed from the ACHECK grouping on the skills screen listing and goes back to the main list which is correct.
Attaching the edited file for all the skills affected.