To make sure we are on same page:
It only happens if the Screenshot Captor is actually on the screen (not in the tray), right?
That is, SC may not be in the foreground, but it's not minimized right?
The problem is caused because of this:
The "after capture minimized" option really should be called "after capture, don't restore from tray", because if the program was visible BEFORE the capture, it will be minimized in order to capture, and then SC will try to restore back to where it was BEFORE the capture.
However, the bug is that when it does that, it can appear in front of another window, even though it does not grab focus.
I will fix. Stay tuned for an update this week.