Not sure if the exact same issue as the OP, but I'm getting a comm menu issue where it stops working after the first command, and able to repro this 100% when using modifiers.
Confirmed on open beta, with F5 & F18 (but suspect this is all a/c), happens whether you use hotas button as modifier (ie. pinky button) or default modifier kb keys (ie. shift/ctrl etc).
The comm menu will work with modifier until the first command is issued - for example, after bringing up comm menu, you can cycle next/prev and use select to go to sub-menus & back without issue. However, once a command is issued and the menu clears, the next time you bring up the comm menu it no longer recognizes the modifier so the next/prev/select no longer work. The modifier itself is still working as normal with other controls, so this seems to be specific to comm menu.
Quick workaround for me is to not use modifiers for these - so any un-modified keys, or hotas buttons will work.
Hope that helps others getting this issue.