It is getting cooler outside...so it may be an exhaust leak. With exhaust leaks though, you will hear it, especially when cool outside, especially when you start the car on a cool morning. It will be a "ticking" sound.
I really doubt that there would be a header issue, as those things are bullet proof.
The 3-bolt flange could have a leak though. Especially if not torqued well at the time of install.
Do you notice any smells? Usually this is the best way to diagnose this kind of an issue.
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