Click in cockpit in different aircraft and the game pauses by inself. Have to hit P to go again. Just started happening recently. Haven't changed anything to do with pause in controls.

 

Any ideas?

So, in the General setting "Pause on task switch" is not enabled?  If you look in the AVSIM CTD Guide, check the discussions on the Uiautomationcore.dll.  If you right click a lot inside the cockpit or open and close the FSX menu a lot, FSX may freeze (not pause) but it might look like a pause.  Hitting the P key will not fix a freeze though and it appears you do not have this problem with freezes (I think as I write....).  There are programs inside the FMC that come with some commercial aircraft (like some PMDG) where you can pause the aircraft at the TOD.  Perhaps this is what is causing your problem.

 

Best regards,

Jim