Most obvious when setting up a pure SRB stage. Happens with all stock SRBs.

This may be the same problem (if not I can open a separate issue), but I'm noticing with 2.0.8 that when I have stages with SRB's and some fuel tanks set to drain with fuel lines, MechJeb will auto-stage when the liquid fuel runs out, even if the SRB is still burning. Here's an example craft that does this: https://dl.dropboxusercontent.com/u/8244638/SRB%20stage%20test.craft

Yes, this was caused by a change in 0.20 that caused MJ to start thinking that all SRBs were sepratrons. It should be fixed already in the latest dev build at http://jenkins.mumech.com/job/MechJeb2/