If you are only changing metronome settings, and playing to that while the Sonar project itself is still in some other time signature, then that would explain the half-measure that shouldn't be thing, if I understand things correctly. (I have never tried that, so if you cannot even do that I apologize).
I write in multiple time signatures all the time in Sonar, and I do an insert Meter change at the beginning of whatever measure I want the altered meter, keep it that way until finished with that time signature, then simply insert a new Meter change at the beginning of the measure where I want the new time signature to be. I don't ever have any measures end up as partially used - half measures - because each measure is exactly as long as I need it to be.
The insert Meter change appears under: Project>Insert Meter/Key Change, and you can tell it which measure you want the meter change to be in. Sonar will then stay in the new meter until either the project ends, OR another meter change is inserted.
Does that help? Or, should I go have some more coffee and start again? :)
Bob Bone