I tried twice creating a subset of 2D class averages by running Select 2D on inputs from a previous Select 2D job. Both times this froze cryoSPARC and I had to restart it (by manually killing all running processes). I am running 3.1.1
@Juha Would it be possible for you to update your cryoSPARC installation to the latest version?
Does the update resolve the problem?