Was the filename extension p.psarck or m.psarck? Files that end on m.psarck dont show up in my Rocksmith songlist at all, only the songs that end on .p.psarck. Alot of the times both files are available.
The "JustInCaseWeNeedIt" fix worked for me. All the cdlc`s were intact and working, however the intro skip mod wasnt working anymore, which is a shame.