Same problem here - strangely enough, when I tried to respec a copy of the same character on Tribble, it worked without a problem. The changes I made to my skills were identical to the ones I made on Holodeck, as well.
Don't know if it's relevant, but the Tribble copy of my character is not as far advanced in the reputation system as the one on Holodeck. Other than that, both copies ought to be identical, except for gear.
Another detail: As part of the respec I tried to remove one skill completely - after the skill window reverts, the skill remains grayed out, and the arrows to in/decrease the skill do not reappear (unlike at the other skills).