Setup: Keyclone.
Movement keys(ESDF) are not replicated (even with modifiers), so they can't be causing the problem. When it occurs, I'm not using the autorun button on any clients (it's not mapped through the keybinds).

I have the autorunning problem strictly in combat situations when things get heavy. Moving the running character manually(having keyclone paused) doesn't fix it directly. When I start jumping and running around for a while(just randomly mashing buttons) it goes away.
It happens very rarely though, only every X hours of playing.

I think Fursphere reasoning is probably correct.

[edit] Smart topic btw!