I really hope it's preferences related, but holding Ctrl (or Shift, which seems to bring up the same dialog) at startup doesn't fix the issue. I've also tried tweaking about every Snap to Grid preference with no difference in behavior. Note also that snap works perfectly for me in piano roll view.
The repro steps you suggested are exact. When I go through them, my Actual Results are that notes are not snapped to their proper quarter-note aligned positions.
I also tried clearing out my AppData\Roaming\Cakewalk\SONAR X2 Producer\ folder and reopening the app, but that didn't help (and it doesn't seem to clear out every preference). Guess I'll try uninstalling and reinstalling X2 again, this time without importing preferences from X1 when I open it for the first time.