When you click first at "Elevation", everything is OK, i.e. QNH is computed assuming new elevation of the start. After application, the "Alt" fields shows altitude as with altimeter in QNH setting, and "Std.Alt" shows the same altitude as before (equal to IGC pressure altitude).
However if you click first at "QNH", although it seems OK (when I click "Elevation" it is recomputed), something goes wrong. "Std.Alt." is wrong and "Alt" shows value, which should be in "Std.Alt.". When I check "Edit -> Flight properties" again, I see that "QNH" is set, but "Elevation" remained the same as before. Moreover this behaviour is unpredictable, because it work this way only when it is first command after opening IGC file.
When you follow this sequence
"Flight.prop., Elevation, OK, Flight.prop., QNH, OK"
everything works as expected. But try this:
"Flight.prop., QNH, OK" (immediately after opening the file)
and you end up with wrong altitude.
SeeYou 
