Perhaps I can describe the problem in better detail.
My usual routine is to start up Super Playlist Surf on its own, dump whatever files/folders I want into its playlist, then start Audiosurf when done. Occasionally I add a few files while waiting for SPS to finish starting up Audiosurf. Not sure if this affects anything. Once Audiosurf has loaded (and I get the green "Audiosurf Ready" status message - I don't even try if it stays on orange), I tell it to "Start Playing", play through the first song, and almost without fail, hitting "Continue" after seeing my score for that song returns me to the character selection menu instead of automatically sending me to the next song in the playlist.
I'm used to this enough that I can take the extra minute or two at that point to close Audiosurf and relaunch it from within SPS. Sometimes that works; usually it doesn't (I get "Registering Window" most of the time). My next step is to close both Audiosurf and Steam and then relaunch both from SPS. If that still doesn't work, I'll close all three apps, and start over, launching SPS first and then Audiosurf, until I get Audiosurf to load successfully and be detected as such by SPS. That usually works.
Today, despite getting green status from SPS after the initial quit and restart of all three programs, it was still behaving like the problem described above - I'd play through one song and then it would lose the playlist, despite SPS showing Audiosurf as ready and clearly knowing what window to launch the first song in when I told it to "Start Playing". At that point, SPS became useless to me unless I wanted to leave Fullscreen every time, switch to the SPS window, tell it to Stop Playing, remove the song I just played from the playlist, and StartPlaying again. That would have been more cumbersome than just picking each successive song from the menu system within Audiosurf.
Before today, I had the hunch that SPS was losing its focus on the Audiosurf window due to steam launching a separate window for its news and updates about new games and such. It'll always do this the first time on a given day that I run steam, which I figured explained why SPS would successfully keep its eye on the Audiosurf window and keep serving up songs after the second attempt (because relaunching Steam wouldn't recreate that update window). It's still worth looking into if that gives any clues as to how this thing might be debugged.
I know it's likely a problem with QuestViewer and/or Steam doing things in upgrade that aren't backwards compatible to the assumptions SPS was making about an older version. I don't know if SPS can be made to compensate for this in any way, but well, there's my analysis of the problem.
