I set it to show at 2 minutes or less, but cooldowns with a duration over 3 minutes don't seem to move to the MM:SS format until 1:30s.

http://i.imgur.com/ibLvRC2.jpg - What it shows as default
http://i.imgur.com/3TYdxhd.jpg - What happens if I move the timer down and then up mid-duration
http://i.imgur.com/RKxUqTW.jpg - Using all cooldowns, notice how Blood Fury (2m CD) shows up properly.

Unless for some reason the threshold refers to the base duration of the CD the spell has to have (EG: 2 minutes = will only show MM:SS for cooldowns that long). But I don't think that's the case since the mode changes at 90s.

It seems that just the 2m MM:SS setting is broken (although possibly every even #'d one is). The 1.5/2.5 intervals work just fine.

I just tried with Nimble Brew and it worked fine O.o