I still have people complaining about this bug on my Steam Workshop page. I thought is was fixed; am I wrong?
In my experience, the problem continues to exist, but is easily solved in-game. The first time (for any given character) that I use any modded skill with a cool-down timer, the timer freezes up. Removing that skill from my skill bar and then re-adding it makes the timer work correctly for that skill for the remaining life of the character. Hope that helps. Note however, that I'm on a Mac, and thus not using the current beta build. I have no idea if the status is the same for other versions and platforms.
It's basically the same for me, using Win version and being in GOG's and Essence's betas. And yes, it's just for modded abilities.
