With PF3 in MSFS I have found that it does not seem to completely trap key combinations.
It really doesn't make any difference which sim you're connected to as hotkeys are handled by FSUIPC
For example months ago I found if I responded to PF3 with key combination cntrl+shift+y it would register in PF3 as it should (Affirm), but also triggered the Y key command in MSFS and put MSFS in Slew mode. Removing the keyboard Y command in MSFS resolved this issue.
Realy not trying to pass the buck here but I think you'll find you can get the same problems within FS20, in the controller section, and is doesn't always pick up all the keys in a combination but reacts only to the last key used. Having said that, you've found the correct solution and exactly what I would have suggested.
I now believe I am running into a similar problem within PF3 when I find myself higher than I want to be during descent phase a flight and I request lower by entering something like “l+9” Now I get the descent clearance to requested altitude but it is it also triggering the HotKey 9 request as well so “Report Position” is triggered. Because of this requesting a lower/higher altitude is fraught with danger. Requesting lower can result in you also requesting higher because of clouds or even worse it can trigger “request cleared to final” or “Divert to Alternate airport” effectively ruining the flight.
Sounds more like a keying issue here. When using the higher/lower altitude request you must press and hold the first key whilst pressing and release the second key. There should be any significant pause between hitting the two keys either, otherwise FSUIPC will just take the first key you hit, action it and then grab the second key and action that separately.
During my last flight, PF3 stopped communicating with me after I was instructed to continue with STAR. This may have been a HotKey was triggered when I was trying to get lower quickly. It may also have been because I had to change arrival runway although PF3 did not issue me with what runway to expect and I guess it would be nice to begiven arrival runway when passed onto approach.
Unfortunately you log file appears to be corrupted. I will have to dig deeper with this and see if I can resolve that first and then come back to your issue. If you don't hear anything from me by the end of the week please give me a nudge just in case I forget
All you oher suggestions really need to go as a separate post in the above 'Feature Request' pinned post