a -.ini.Backed or -.ini.Base version are unknown to me
These could be backups of any additional programs. (any Modmanager or ...?) We cannot support such programs.
decisive for us are the Enderal.ini and the EnderalPrefs.ini under:
... \Documents\My Games\Enderal)
Do you have any mods installed, if so, which ones?
Deactivate or better uninstall them, we can't support mods, only the creator can do that.
Try it with a resolution of 1920 × 1080 (FullHD /16:9) to see if these problems also occur.
Setting in the EnderalLauncher \ base-setting : frameless window mode or full screen mode with the option OneTweak "off".
maybe you also have some problems with WideScreen
The solution should then be here:
you are probably using a different screen resolution than 16:9 / 16:10
you should either adjust your resolution in the EnderalPrefs.ini "... \Documents\My Games\Enderal" or via launcher to max 2560x1440,
or use: https://www.flawlesswidescreen.org/]FlawlessWidescreen