Well i've found a work around that simply requires some specific conditions to work, so I'll post for anyone else having this problem.
You need to open the game with no other windows open or minimized, otherwise it will think they are active and will make the task bar appear near the bottom of your screen causing the issue. Also the game needs to open the first time into full screen, if it doesn't, make it full screen, quit then open the game again, it should launch in full screen and be stable. DO NOT alt-tab, as this will revert it to having the same issue and you will need to exit the game again to get it back to normal. Hopefully this will help anyone else who was having this problem.
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