the 2nd is fixed for the next update. For the first I cant reproduce any issues so could you send me your settings file (help/ support/ view settings)
Thank you! The latest patch fixed the first problem also.
"Auto-Tag by Album" do not apply to cue files.
it wont update the cuesheet if thats what you mean
MB applies the changes to media files (flac, ape... etc) but does not change the cue file.
cue > Auto-Tag by Album > Applay tags;
The result; In "playing tracks" and "Library" will show MB change, open the "Edit cuesheet" and make sure the changes are not applied.

Sorry for my bad English.