Xbox 360 Controller Calibration issues

So I've had this problem over the last week or so where when my controller powers down either due to putting it down and the batteries going loose long enough to power off or from powering down due to inactivity. Upon powering up the controller again ALL of the binds are completely wrong. For instance left analogue forward and back normally controls the character. Suddenly when this happens my right analogue left and right is now my forward and back. The only fix for this is to completely re-calibrate all of the controller buttons each and every time. I believe the controller is working correctly since it continues to show proper button calibration from the windows controller UI, and the controller immediately is able to be reconfigured in FFXIV's in game calibration tool correctly. Each button maps as expected. This appears to be some issue with the way FFXIV is handling the re-initialization of a controller while the game is running or some other similar issue. Could you guys please look into this problem. It's extremely agitating to reprogram my controller because I put it down for a second.

Just now I repeated this issue. On the main screen I was using my dpad to move through the menu's. I popped the battery off the back and popped it back in. Turned the controller back on and all the binds were messed up. I can't even change batteries without this problem occurring. This wasn't the case until very recently so I believe this is a new issue.

I've been using this controller on Elite Dangerous for over a week now and do not experience similar behavior from the controller at all. This leads me to believe this is a FFXIV issue.