On the "Pre-Capture Options" tab, do you have "Hide Main Window" unchecked? Try checking it if so.
that works, thanks mouser
Ideally, would be nice if it were possible to keep it open, but I'm happy now - I always forget to close it manually.
 Another minor related bug:
with "Hide Main Window" checked, if I press escape before taking a screenshot of selected arrea, the SC window jumps to the front.
Dunno whether this any help:
If I check "Hide Main Window", and then uncheck it shortly later, it works mostly as expected (it needs a restart to change back to bug-behaviour described in previous post). i.e. SC stays in the background. But same problem as  above