I was trying different options using PF3 yesterday and found that the standard 'Roger' hotkey (C-S-\) wasn't working, all of the others seemed to be OK.
Recently I have mostly been using VCP 2 while getting used to various aircraft systems, for a change I was in VCP 1 mode so needed the 'Roger' key.
(I know that this same issue was mentioned in another thread recently, but I think I may have got to the bottom of the problem and found a good solution)
I spent quite a bit of time looking to see if any other software was trapping this combination, but couldn't find anything - so I turned on FSUIPC key logging and tried again.
What I quickly saw is that the \ key on my keyboard sends a scan code of 220, not the 92 that PF3 expects - this is for a standard layout UK keyboard.
I then remembered that I had a similar problem some time ago with the 'Say Again' hotkey, and I had resolved that by re-assigning the key (PF3 expects 61, but gets 187).
I fixed my issue by manually updating the pf3.ini file to give the correct values for Hotkey11 (3220) and Hotkey 13 (3187) - this uses the documented key combinations on my keyboard.
Subsequently I found that it is possible to persuade PF3 to update pf3.ini to reflect the correct keyboard scan codes by temporarily assigning each key to a new value ( I used Control-Shift-[ ) and then re-assigning the default key combination.
I hope that this information is useful to others.
Regards,
Martin