click "do not isolate again" yet the message repeatedly comes up

I started using comodo on this PC because an internet check for a root virus showed that comodo recognized the carrier program. It did nothing for the root problem, but I thought that warranted a look at comodo.
I would have it pop up the message about isolating a program, click on “do not isolate”, exit the program and try again and the message would pop up again. What am I missing (and nothing in your pages of document about sandbox to explain this - yes, I looked). Thanks!

If you feel you may have an infection, this is a great article. How to Know If Your Computer Is Infected

As for the continual sandboxing, if an application changes from run to run, it will be continually viewed as unrecognized by CIS because it uses file hash for recognition.

To get around applications like this, you can go to the Defense+ → Trusted Files list. Click the Add button, and Browse to the application in question. Click on the application name, and select Use file names instead of file hashes (not recommended) and click the arrow to move it over to the Selected Items column. Then Apply your changes.

You should only do this with applications that you are sure are safe.

This fAQ may also help: Removing files from the sandbox and handling sandbox alerts.