That is a dozy of a bug. Never ran into that in my playtesting. Do you remember what upgrades you had purchased?
Yeah, that particular upgrade was a punk to code. I figured if something broke, it would be that.
Oh well. While I've been reworking it, I've found a handful of spelling errors and some mismatched portraits, so fixes all around. Should have a fix implemented shortly. Let me know if you find anything breaking down.
So it does. The final tier of the "Crippling Seal" upgrade borks up for some reason. Which is exceedingly odd, because all the other tiers work just fine, and they are coded the exact same way. Hmm...
EDIT: There we go. The final tier of the skill was flagged wrong, so it was getting lost. Easy fix, I'll post a patch in the morning.