Problem solved with a system restore.
Just to clarify for anyone who reads this, The options were present on the ISE gui for changing rules, but there weren't any rules showing there. This is why I thought ISE might have created them in the untrusted certificates folder on the computer.
I checked another computer in the mean time, and the same two are in the untrusted folder on that computer, so I assume those are there from Microsoft and nothing to do with the blocks. Still don't know where the setting for this would be for me to have regained access. I looked in the Google Chrome settings and everywhere else. Got e-mails back restored, so if anyone has an answer I would like to know where these settings are.
Also, is it not troubling anyone else that Comodo is finding untrusted certificates between PCs and Microsoft Outlook, Twitch, Amazon, and Yahoo!? I would really like to hear more on what this could potentially be, and thanks for reading.
I have a post up at the Comodo site if anyone actually cares about this:
ISE is Blocking Sites after I Selected to Block Certificate - Help - ISE