I'm not sure what "picked up the same internet settings as IE" means.
By default, Chrome respects IE's proxy settings.
Chrome uses different settings for HTTPS ciphers and whatnot.
However, this shouldn't be relevant at all, insofar as Fiddler would hide the difference between Chrome and IE here because it's intercepting the secure traffic and regenerating the traffic itself; nothing should be different in terms of the HTTPS handshake coming out of Fiddler.
A PCAP is probably the way to go.
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