When I use auto monitoring, every single https site doesn't load in chrome - and I'm on the windows side.  I've got the most current install 6.0.1.64 and this is really frustrating!

Check the version of chrome your running to see if your affected by this:

https://www.jaksta.com/support/windows/kb/jaksta-media-recorder-auto-capture-and-chrome-580302981-released-04192017-6000170847

Nope...I'm not on that version of chrome - I'm on 59.0.3071.29 (Official Build) beta (64-bit) 

But Also just tried using Firefox 45.0.1 and got the same thing.

It ONLY happens when I turn "Auto" on - every SSL site gets the same response.

Your build is a later build, so you will be affected by it.  Temporary solutions are listed in the article.

For your firefox issue which is a different error.

https://www.jaksta.com/support/windows/kb/firefox-not-loading-https-pages-when-monitoring-is-on-mentions-sec-error-bad-signature-6000040003

Unfortunately that fix was done and I still got the same result.  

Please provide debug logs with AUTO on and trying to load google.com as per

https://support.jaksta.com/discussions/topics/6000009063

I went to google in chrome, and also in firefox.  It was able to load in firefox, but not youtube.  On youtube, it gave me the same error - connection not secure.  

I hope this helps.

Looks pretty strange.  You are using a very old version of firefox. Something is corrupt.  Upgrade to the last firefox which is v53 and uninstall, including removing all settings and reinstall JMR.