I have the same issue and I could not reproduce it consistently. For some projects, the export is just fine, for other projects there is an unwanted "fade-in" in the beginning.
EDIT: I have narrowed it down to one plugin: Black Rooster Audio's "VLA-2A Mark II". This guy introduces reproducibly the initial "fade-in" in the Export. Not so its predecessor, the "VLA-2A", this one works just fine.
So, it seems it's not S1's fault, at least not exclusively.
I haven't had this issue with Ableton, though, when using the same plugin. Never did it introduce an initial fade-in on export.