OK, I got back some info. It seems that reliable sync during multitrack playback can only be assured when the sample rate of the multitrack files matches the output sample rate of your audio interface. Stage Traxx currently always uses 44.1k as the internal processing sample rate. So everything works fine if your interface is running in 44.1k and your audio files are also 44.1k. If the interface or your files have a different sample rate then the multitrack sync will be lost sooner or later and there is nothing to be done about it (except restarting the app when that happens).
I think this does confirm what @Jb6767 saw in his tests.
So what I will try to do in version 3.6.5 to make this a bit more flexible is to let you choose which sample rate you want to use. You can then choose between at least 44.1k and 48k. Maybe even 88.2k and 96k although this is in my opinion only a waste a space and cpu for a live performance. If an audio interface does not support the chosen samplerate, the app will fall back to a samplerate that is supported by the audio interface and use that.
Additionally I think I will add a warning when you add tracks to a multitrack song that do not match the current samplerate. Maybe it will also make sense to display this warning in the song list.
In any case you will have to decide which sample rate you want to use for all your multitrack songs.