This is sort of a dual Windows/ FFXIV problem. You can fix it by figuring out what is making the device manager refresh and fixing it (I personally have managed to do that on 1 of 2 PCs running the game, both of which were exhibiting the problem -- one still is). It really shouldn't be that way though and the problem can be amazingly tedious to diagnose properly.

As nexen observed in the topic you linked (final post), the problem seems to arise from FFXIV checking for a new controller whenever the device manager refreshes (most games don't do this apparently though I don't know the reasons either way). It will unload your controller and reload it with whatever settings were present when you started that session. Most likely the controller was already configured, but you'll notice that if you start the game with a bad configuration (as wireless controllers will do if you turn them on after starting the game), calibrate in the settings menu, and then play, the controller will revert to the 'bad' settings the first time the device manager refreshes.

Most of the information is unfortunately useless to players who are powerless to fix the problem and SE doesn't seem to be getting around to it anytime soon. Most likely something radical like reinstalling Windows would fix the issue, at least for a time, but that's a huge hassle and shouldn't be necessary. Best case scenario (probably) this problem is absent from the DX11 build set to be released alongside Heavensward, though I suppose it's possible that SE addresses it specifically even for DX9 users.