I am not sure what could have caused it but I would assume that it's a bug that only could happened when using an old save i assume. Since some code was change over the versions i think that would be the cause for it. Its nothing that should happen when playing a fresh game in the current version at least. Sorry for the inconvinience!
That most likley was caused by the save order script that runs now after the transformation skill and loaded your last saved party.
Did everything return to normal after you just removed all other party members and added them to your party again?
Also the transformation skill got changed in 1.7 or 1.8. It now dont levels anymore but can instead be upgraded at the dojo. So i could remove the cooldown from it when used in the overworld.