Just got the devs to acknowledge the whole thing, and it is now a known issue:
That's very obscure, I think it's probably a bug that you've identified though as I can't see how this would be normal behaviour. I've added this information to a bug tracker that discusses a very similar issue and hopefully we can solve it.
Thanks for all your help with this, it's really awesome to be able to discuss stuff like this directly with people like yourself

If you'd like to add more information or if you'd like me to keep you updated with anything then just reply and let me know.
Fly safe Commander.
CMDR Vanguard
Elite: Dangerous Customer Support Wing
In the meantime, it seems the whole "disable a cpu core, then re-enable it" thing works, but only to an extent, This might be a serious software bug