It seems that since I upgraded to bisect_ppx v1.4.0, our ocaml code is always instrumented, even without setting BISECT_ENABLE=YES.
Downgrading it back to v1.3.4 fixes the issue.
I unfortunately didn't manage to reproduce this on a minimal example yet but I'm working on it, I'll get back to you as soon as I'm able to do so!
I think it was worth mentioning anyway in case you'd be aware of a recent change that might have somehow impacted -conditional behavior.