When you go to Ekos Align, Options, the screen will be too large vertically, to the extent that the buttons on the bottom will not be visible. This means it is impossible (or very hard) to save the settings by clicking Apply or OK.
This happens to me on a laptop with 1280x800 and another with 1440x900.
I think the reason is that under Astrometry Index Files, the list is too long, specifically the 2MASS list.
Is there anyway to improve this? Such as adding scroll bars and making the whole thing fit in less than 800 pixels vertically?
These bugs and I expect others are bound to appear on non-KDE systems. I think the best place to ask is XFCE for now since this is what you are running, maybe they can offer a solution.
When in that window, and you want to save the settings, do the following.
Press Alt, then left click anywhere in the window, and hand icon will appear. You can then move the window up until the buttons appear, then clock the Apply or OK button.