SM5 defaults into step timing mode IIRC, I'm not sure why Jason set it up that way. It should be easy to quick-fix it just by hitting T to change modes and setting your offset again.

If you have sync problems please tell us at stepmania.com, on IRC, or on the bug tracker. This stuff is really important and we do try to fix everything we can!

I know this is a bit of a bump or whatever, but depending on your version of Stepmania, (I'm looking at you Stepmania 5) weird stuff happens with the Beat 0 offset ALL the time.

All the time.

I honestly don't know the cause, but your beat 0 offset can change without manually inputing it or even auto syncing it, and it's incredibly annoying if the song is already synced. This tends to only happen in edit mode, so EVERYTIME you make an edit in Stepmania, especially Stepmania 5, you should make a note of the beat 0 offset when you first start working and when you finish working and make sure it's the same both times, assuming you didn't tweak it while you were working.

P.S. Beat 0 offset can be different depending on the chart. It is not global to the song. In other words, Hard difficulty can be off sync and Expert mode but bo completely synchronized. Just make sure all your difficulties have the same beat 0 offset as opposed to just syncing a song and assuming all charts are synced. A hassle I know, but it has happened to me.

I fixed the issue. It was directly related to the beat 0 offset There's a really short period of silence before the song, then a quick 8 beat into on a hammer dulcimer or something, then the main part of the song starts. I had the beat 0 offset set to the main part, not the beginning of the intro. I added 8 beats, retimed it, and everything is grand now.

I used the clap (and originally a run of 1/4 notes for ~20 measures) and got it in sync, and when I play the song it's still in sync. The difference is when the arrows start. It's something like 1 beat off. I linked to the zip with the mp3 and the SM file so you can try it out. Boggles my mind.

Wha? That's strange. Beat 0 offset should have the same impact in edit mode and game mode.

Have you tried using assist tick edit mode? I will try to sync up my song in edit mode by turning on assist tick and autoplay. I listen to the 'clap' and how in-sync it is with the song. Use F11/F12 to adjust the offset until it matches up.

Don't use your vision to sync up a song. Monitors and other things can produce a lag that can mess you up. Just use your ears, listen to the claps and the music and adjust until they overlap correctly.

I know this doesn't directly address your original issue, but I still hope that it helps with syncing future stepcharts.