I've done this three times now, and it has happened every time. I assumed the first time I must have chosen the wrong file but I have not.
Here's what's happening; I have an iPad connected to iTunes on Windows and a local hard drive with multiple multitrack songs. All confirmed to have the correct files (these all worked a couple of weeks ago in the MultiTracker app).
I drag three folders over to FileSharing in iTunes into the ST3 folder, alongside the Multitrack-Files folder. So in the iTunes Fileshare view, there are four folders - Song1, Song2, Song3, and Multitrack-Files.
In the ST3 app I Create Multitrack Song. Name it SONG1 and configure the click, cues, etc to the files from the Song1 folder, all is good.
I create a second Multitrack song, name it SONG2 and configure the click, cues, etc from the files in the Song2 folder, which I confirmed each and every time.
Now, when I play SONG2, I hear the click and cues from SONG1, every time. SONG1 plays fine. What in the world is going on?
<EDIT> Additional details. I can delete SONG1 from the list, and SONG2 still plays with the wrong click and cues. If I click File to replace them, it opens up at the same folder it was in before for SONG2, and I choose click and cues, and then it plays SONG2 correctly (it's now the only song in the list). I add SONG3 and it seems to play fine...when I go back and listen to SONG2, now it's bass track is from SONG3.