Using a recent (couple of days old) autobuild of 6.01.02, I created the default monsters for a dwarf and an elf. The skill points seem to be applied correctly, but the extra points needed (and granted as FREE:YES) are triggering the "Too many Skill ranks chosen - some need to be removed." messing in the Things to be Done area.
This seems to be different than the 1-off and the default rat one at DATA-897.
What sources are you using?
RSRD 3.5, PCGen OGC, and Homebrew (no changes).
I've noticed similar problems when using skill points from human preferred class bonus. If I assign one, then delete it, then try to re-assign it to a different skill, it tends to confuse the "things to be done" area.
I have a kit that grants a choice of 1 craft and 1 profession skill to a character for free (I use the FREE:YES tag in the kit)… This works as intended, the skills are granted..
However, on the summary tab, when the character has spent all their skill points they normally get and the kit is applied, it says that they’ve overspent their skills.
I thought maybe it was me, but I have 4 characters from my PF game I keep track of and they all have this issue… If I go in and manually remove their choices from the kit, the ‘warning’ on the summary tab goes away..
This affects version 6.01.08 (not an option for 'Affected Version(s)' so I added 6.01.07 up top as well)
Skills to-do is now based only on the remaining values in he levels list on the skills tab.