Maybe you're not supposed to (normally) move whilst a progress bar like that is happening?
There not appear panels to interfere player movement in TF2, when generate nav file.
In Cs:s, progressbar panel "block" player buttons and bring up mouse cursor.
This stop player.
But can bypass by closing panel with alt+F4, but while nav file is generating, it will bring panel back more than once.
Updating showing progress status.
Threaded Mode