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So I've recently tried to make a Talrand commander deck and put some "free" counterspells in to protect the merfolk. They don't seem to work.
Force of Will, Foil and Thwart seem to have no effect at all, even tho their alternate-cost-paying works as it should.

I can't confirm any of these.You may have an older version.Anyway without a savegame and more info I can say only that this is unreproducible.

Actually, as I've started testing it furtherly, it indeed seems random. Most of the time they do work, tho. Will continue investigating it.

http://www.filedropper.com/thwartnotworking

Here's a game in which Thwart refused to counter a Pelakka Wurm.

Your savegame has to be in the same turn the bug happened.The one you provided is between matches.

http://www.filedropper.com/thwartnotworking1

Sorry for wasting your time, now it should be the correct replay replay.

http://www.filedropper.com/thwartnotworking2 and one more.

I can't quite get Force of Will or Foil to bug, but I swear at least the Foil refuses to respond sometimes, too. Not sure about Force tho; I think I made it bug once but it works fine every time now. Funny thing is that AI has no problems with either of those.

Worked just fine for me.

Maybe another manifestation of this?