I had/ have this problem (fixed it on one PC and it cropped up on another) or some variant. The post you (Rufalus) linked explains the steps that I took to fix it on my office PC. For me it wasn't quite as simple though. I had to delete several hundred Storage volume shadow copies that seemed to be multiplying out of control. The controller stopped responding every time one was created (no idea why they were being created to begin with). I also had to disable shadow copies, with the implication that system restore points are no longer created (I don't use them anyway).

For me the controller would 'unload' and continue whatever input I had been giving it rapidly for 2-3 seconds, meaning I would continue walking/ running in a particular direction, camera would spin, cursor would fly through menus much faster than possible manually, or a button input would be repeated ('X' for example). The duration of 'uncontrollability' seems to be tied to the performance of the machine. On my office computer it was 2-3 seconds, but on my home PC (a much better machine) it's only .25-.5 seconds (as such I haven't spent hours fixing it yet). I say that the controller unloaded because if you were to make any changes to the controller, or to which controller you're using after the game booted up, all changes would revert after the 'incident' (meaning if your controller was poorly configured or not plugged in when you booted up the game that session you'd be stuck with keyboard controls to either get to the config menu or log out). If you started the game with the controller properly configured and connected then it would just revert back to working order (though you may have walked into Twintania's flame wall or off Titan's cliff).