I did this on a song a week ago with no issues. Today it doesn't work. I've tried both the Smart Tool and the Select Tool. The transient markers in question are active. Can't think what else might be preventing this. Any thoughts?

Weird. The first transient marker on the track wasn't until the 3rd measure of the song. Audiosnap figured that the first transient was beat one of measure one. Given that this was so far off from the song's tempo map, all of the beat markers were locked. I copied the downstroke of the guitar chord from measure 3 to measure one, Audiosnap recalculated everything and now I can move beat markers. Yet another workaround, but at least I can work with it now.

I just ran into this problem too. I was setting project tempo to click and darned if the first few measures are WAY off. Can't drag those darned measure markers there for some reason.
 

I too get this, plus lots of other bugginess with Transient Markers...
 
I submitted a bug report for this. Hopefully the Bakers will address this in the next version / update.