Its a bug in the software. (Sorry Spoon. I should have reported this already. I forgot.) The scanner window always seems to pop up in the upper left...
We can look at it yes, it could be a case that indexes do not always match track numbers (in that a track could contain multiple indexes), this I do...
Because often people have albums which have the same name, such as 'Greatest hits' and no indication they are compilation albums. At a guess 99.999%...
I have 17.3 installed and have tried producing a cue sheet, but all of the track's output with "INDEX 01 00:00:00" rather than correct disc location....