Stuck on 100% at JS_keypairgenerator.class

After letting CIS run for over two days it got stuck at 100% on JS_keypairgenerator.class. I had no option but to force a Shut Down and restart. It also slowed a slow machine down even more. It also wouldn’t allow Retrospect to run its backup scripts.

Make a scan with malwarebytes antimalware free.
It seems you have a problem on your computer.

If you are looking for a small resource footprint antivirus, avast (free version) is running fine with comodo firewall and defense+. (If you are running windows 7, you should read about the use of the avast webshield, as it can have a “conflict” with comodo firewall).
To substitute a regular antivirus, you can reduce the components of avast while installation. Datasystem protection is the basic antivirus function.
BTW, with any installation, use custom installation! You avoid to get “surprises” after installations, and you make the choices.
And make the settings! For example, you can set that files are not rescanned often if they do not change. Autoquarantine should be usefull to disable (in case of false positives), etc…

But first get rid of any infection on your system, before you install a new guard antivirus.

Apparently cmdagent.exe (Comodo Internet Security Helper Service) has crashed during the scan on that file.

If you have the time and energy please consider filing a bug report in the Bug Reports - CIS board following the format as described in FORMAT & GUIDE - just COPY/PASTE it!.

Reporting of bugs is strictly moderated to make sure Comodo gets clear bug reports. So, please make sure you closely follow protocol. That way your report will certainly be seen by Comodo staff.

Also follow How to determine which file is causing a manual scan to hang to determine what file was causing the scanner to be hung. Please add this information to your bug report.

As to the problem with Retrospect. Can you post a screenshot of the D+ logs?