I don't have any ideas, but I wanted to chime in with a "me too."
Mine is also a '99, and it does this noise change on every cold start. I haven't noticed whether it does it on warm starts, but I will look for it now.
It doesn't seem to have any effect on how well my engine runs.
I had also been guessing that it was some accessory kicking in, like maybe the air pump.
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