I have the anti virus disabled but it still pops up when I start programs.

the antivirus is only a module of the suite
the popup you are getting are from defence+

if you wanna stop it popups do not disable it, its the principal comodo securty feature.
intead set defence+ to training mode

It popped up asking if I wanted to quarantine it though.

When the cloud look up of D+ finds a file to be malware it will notify you about that.