One not-so-quick update later...
Not quite. It takes "input focus" away from Mail -- keystrokes are directed at the "Display Text" window -- but Mail remains the frontmost app. Importantly, the selected email remains selected in Mail, which is what's needed for both the Token and the menu manipulation.
- Mail does not need to be the frontmost app and does not need "input focus" for the
%MailRawSource%Token to be evaluated - Mail does not need to be the frontmost app for a targeted (rather than "Select menu in Front Application") "Select or Show a Manu Item" Action to work
In the KM Editor (so KM is the frontmost app) try "View"ing the "Display Text" Action
...and "Try" the "Select 'Reply'..." Action
...and they should both work.
In short -- I can't reproduce the issue here so it looks to be something specific to your macro and/or setup rather than a general KM/Mail problem.
As usual, you really need to write and then post the most minimal macro that will demonstrate the issue. Nine times out of ten just writing a new demo macro and the explanatory post will lead to a face-palm moment when you realise what you were/won't doing in your main macro that caused the problem -- what's known as "Rubber Ducking".