I've noted the issue - it appears to be bound to either framerate or resolution. I'm leaning towards the latter (unsupported resolution of one monitor versus the other). My two solutions were either:
A. Disable being able to change the resolution of windowed to whatever you want and force it to be the 'accepted monitor resolutions' found in the settings.
B. Change the level up to not be 'hold', and instead a 'click' to immediately dump 'X' Essence in (either all that you have or enough to level up).
I have gone with the latter, in hopes that the game can continue to support any windowed resolution (I personally really enjoy having the window to not take up an entire screen, and have spent a good deal of work making the UI adaptable to most resolutions). Hopefully when this is implemented in the next version, the issue goes away... Though I believe someone mentioned some other issues with other buttons as well....
Oh well! I hope this solution is a good step forward to crushing the bug out altogether.
And thank you for the report!