Additional information:
https://forum.renoise.com/t/samples-bug-when-loading-with-jack-sync-enabled/42893
In this case, it is not an override of any value in jack transport. It is the random BPM generated by Renoise itself that takes over when jack transport is enabled.
jack transport by itself has nothing to do in this problem. Enabling jack transport confuses Renoise internally. The value does not come from jack transport. This is what I have seen.
I can submit a formal step-by-step test report along with a sample to test with, if that makes it clearer than plain, discussional, text.