Hi Dave,
I smacked myself in the forehead when I realized what the issue was: elevation adjustment.
I have KEGE (ORBX) and was taking off from there when I saw the cockpit windows wouldn't open, just like when you're airborne. So later I started a flight from KLAX (BP Sims), I click on the windows and they opened just fine. So if you're using airport add-ons, and they are implemented with "elevation adjustments" like ORBX's KEGE, Captain Sim's "ground protection detection," doesn't let you open via the click-spot, but the animation panel bypasses that. So in other words, it works fine with FSX or a ground level airport add-on, just not well with some elevation adjusted add-ons.