1/ You have the "alt" status bar enabled. Kill it with fire. (bottom menu, rightmost tab, first option).
2/ I think you may be the first user *ever* to use this old, old, old feature?
. (Barely joking here ^^). I don't quite remember how it's doing that, but that's probably tied to old and messy CRe guts. @poire-z may remember more about it than I do.
As a quick workaround, you're probably better off not doing that, and instead using a larger contrast value (the option right below the aforementioned messy bold toggle ^^).
Or, using better fonts or larger font sizes?
3/ No, it's the actual eInk refresh black flash. That setting only applies when actual text is displayed (i.e., the reader, or dict/wikipedia popups for instance), not UI elements.
You haven't told us on which device you're using KOReader, but the fact that you actually see this option should imply that it is some kind of eInk device, so you should be somewhat familiar with the phenomenon.