The game it-self runs great, no slow-down or anything. So now I'm stumped and wonder if recent updates are hurting the synchronization? Even tried settings in game that delay the notes, but nothing worked. Tried several versions of Wine and configurations. This has never happened before in PlayOnLinux/Wine so I start troubleshooting the problem. the song starts in time with the notes but quickly goes out-of-sync. I played it recently and found a problem. My family and I would play it from time to time and I even migrated the virtual drive (wineprefix) from one computer to another computer.
I posted a guide years ago on running Frets On Fire FOFix in PlayOnLinux with Xbox Guitars.