Ive had this happen but it was always tied to a certain song. The only way to fix it was restarting rocksmith. There are still some songs in my library that do it and I keep a notebook to mark them and remove them or see if there is an updated version to download.
Best purchase I made in a long time. I have around 4800 songs and Im all over the place with tunings when I play. I just hate that I only discovered it about 6 months ago.