It took me a very long time to find this very vexxing problem. I'm reporting it here for review and/or comment/fix. This has been plaguing me for months.
I have found mapping mouse left, mouse right, mouse scroll up, and mouse scroll down, to be VERY helpful when in VR mode. However, with limited buttons and many many things requiring them, I have resorted to a logical modifier setup. I have "default" with no modifiers, and I have a modifier for "flight" and another modifier for "combat/action."
On the side thumb 4-way hat of my stick (hat #4 on CH Fighterstick Pro) I have default set to mouse left/right/up/down. However, because these are mapped it does NOT play well with other modifiers. The problem is it's sporadic in how it fights back. I have mod7 (throttle) set to my flight options. Thus this handles flaps in/out, gear toggle, and wheel brakes toggles on that same 4-way head. Never had any problems running this with mouse buttons in default. However, I have mod9 (throttle) set to combat/action options, and this includes china hat aft/fwd as well as speed brakes open/closed. I ran into SOOOO many problems with these not responding. No matter what I did.
I could not get it to narrow down the cause of the problem. Then even after I cleared binds but left the UI layer keys (where the mouse buttons are) it would not let me remap those speedbrake and china hat options to even non-modified buttons by themselves. For example, if "action" and "speed brake open" was changed to just non-modified coolie hat up, it still wouldn't work in-game. It kind of saved the screwed up nature of that command.
I used hand editing LUA files, I used in-game control mapping, and I used JoyPro in various ways to test and narrow down WTF was going on here. I found the culprit just today. It's definitively the buttons mapped as mouse buttons screwing everything up. As soon as I cleared those out, every instance, every saved input setup I was playing with and saving/swapping to (about 5 total) all worked again perfectly.
Sub-note: I'm not sure if this problem is based upon the nature of mouse clicks and maybe it thinks they're special and can only work with maximum of 1 modifier in-game, or if it's an issue with these being mapped in UI Layer instead of plane layer. It is possible that the mouse buttons thought they weren't being modified because they were in click mode or something. I saw the crosshair come up a time or two (not reliably repeatable) when I was looking at my air brakes trying to get them to open. I tried clearing the 4 mouse buttons out 1 at a time to confirm, and each mod9 + that-combo worked as soon as I did each one. I went back, did another, hit OK, tested, and went back and did the last two one at a time. In each case, it was the mouse keys preventing the modifier mapping from actually executing.
I also have a third modifier on the joystick pinky button (not used as much) that I tried to map things to in order to determine if the problem was based on getting a modifier from a different controller, and this had the same problems, albeit while still allowing the mod7 modifier to function with flaps most of the time. It was very sporadic.
Planes tested in, confirmed in, and corrected in (via deleting the mouse button default mapping and seeing immediate positive results seconds later): A10C, A10C II, F16C.
P.S. I would very much love to get this fixed so it works like any other modifier mapping.