kOS uses its own homemade system for dealing with keyboard focus and click detection, but this system does not make use of the ClickThroughBlocker mod that all of Linuxgurugamer's mods use.
Looking at the code for it, the way that ClickThroughBlocker is designed only really works well if all the mods are participants in its system. (So essentially once some mods are using it, all the other mods have to also be using it too.)
If this is addressed, then Issue #2694 should be tested with this change. I doubt it's the same problem, but because it deals with window focus, one could affect the other.