When a multi-track file (e.g. a flac file with embedded cue sheet) is added to picard, it sees it as a single file (although it does show the cuesheet-related tags). This means it won't scan/lookup the embedded tracks separately, nor is it capable of updating the tracks's metadata properly.

Ideally such a file would automatically become a cluster; I suppose that underneath, picard should use "filename + subsong index" instead of just "filename" to identify entities.