Joystick disconnects on FSX

I have a very perculiar problem that I have not encountered before (well FSX is full of those, isn't it?)

When I press 'fly now', FSX enters full screen and loads the flight as usual. However, when the bar hits approximatelly 80% FSX enters windowed mode. By the time it loads the flight, the top of windowed FSX is grayed out (like when you have multiple windows over your desktop and the one on top has a blue titlebar while the rest are grayed out), meaning not selected. At that point, my joystick (MS FF2) seems to be working fine. Keyboard shortcuts aren't working but that's 'normal' because FSX inexplicably loads on a non-selected window. What is strange is that although the FSX window is not selected at that point, FSX is not on pause. However, if I click on the FSX window my joystick disconnects from FSX (no joystick on the FSX controls menu) and I have to restart FSX to connect it again. Joystick does not disconnect from windows at any time. It is just FSX.

So, it seems that I have described two problems:

*FSX always used to run on full screen. I never needed to select full screen after the flight was loaded.

*I never had any problems with joystick disconnections in the past. Now I do.

HOWEVER, I think that the two odd behaviors are somehow interrelated, but cannot be sure about that.

This drives me crazy and I really cannot think of any solution (neither could I find any online). Any suggestions?

PS. My version of FSX is the acceleration pack and my OS is Win 8.1. I have several add-ons, including REX, ORBX, Active Sky, Pro ATC X (currently uninstalled), several airports and several aircraft. Also, Steve's fixer for Direct X. The aforementioned problem(s) started recently and initially I thought that it was Pro ATC that was causing it (that's why it is still uninstalled) but it wasn't.