Keyboard shortcuts disappeared from time-to-time in 2.1.3, but they disappear from moment to moment in 2.9.91. Almost anything and nothing makes them vanish. Here one second, working this sentence. Gone the next, working on the following sentence. Changing the font used to display the source is one sure way to wipe customisations, but this is far from being the only cause. It is just one that I've been able to pinpoint.
I cannot reproduce this problem with frameworks 5.41 and Kile from git (commit a2ab287785dc71319f0795a2d206c51ce83e939e). Please update your set-up and check whether the problem still occurs on your machine.