If you use Tagscanner to scan cue based folders it only finds the linked flac/wav, and the Jukebox doesn't use the cue.
On TestFTP there is a "prototype" Cue Jukebox which shows what can be done if this can be corrected using post processing.
http://www.mede8erforum.com/index.php/topic,8742.0.htmlThe file is "Cue Jukebox.rar"
The post processing would do as follows;-
1)Check the tracklist output from Tagscanner for albums with a single flac/wav.
2)Go to those folders and check for a cue file.
3)If a cue exists, use that to create new cue files, one for each track in the cue file. Give each the name of a track, and move all preceding track entries in the cue to the end of the cue file (see prototype example). The File Entry line in each cue should point to the same flac/wav. You don't need multiple copies of the same flac/wav!
4)Modify the tracklist.xml and convert the single flac/wav entry for the album to a multiple cue file entry instead. (see prototype).
The Jukebox can then be scanned as normal, and the modified tracklist will create a jukebox using the multiple cue files, and not the single flac/wav.
In testing the prototype I have found 2 things:-
1)The x2 won't play cue....and can't run the prototype.
2)The x3d has a horrible cue track change stutter the x2 does not have..even when using cue normally.