[Farhoof]

Does it help to disable "Disk Cache" (set to Normal).
I don't think I have experienced this, although I never use the mouse to set clip gain, I mostly nudge with the mouse wheel (or set breakpoint with the mouse, but I don't use that little left bottom fader). I set clip fx during playback all the time though, never had any issues other than the first change is never applied, I have to press twice.

As a consolidate workaround, you can use the gain plugin, set it to individual files, clip by clip, and handles to 'whole file'. You'll keep everything you had, it just takes up more disk space.