Hi Duskao,
First, as for BOClean integration with CIS it is still in developers ToDo list if you read some articles here about CIS and BOClean.
In addition you are using firewall only as you stated. So, currently you need to run it as a separate application if you want protection provided by it.
You said that
... downloading the update file seprately then putting it into the proper folder...
Are you saying that pressing <<Check for Update>> button from BOClean window produces the same Error?
You may read the following case.
Is that what you having?I think there were few similar discussions in the past as well. Just Search the forum.
https://forums.comodo.com/comodo_boclean_antimalware/boclean_encountered_an_error_and_needs_to_close_screen_shots_included-t30355.0.htmlIn addition you may try to reinstall. Usually that goes smoothly as per instruction.
Irrespectively I would shutdown it down from SysTray; then Stop and Disable its Service; uncheck Startup entry using, say, Autoruns; Reboot and then reinstall.
My regards
P.S. Personally I never encountered this problem neither when having SP2 in the past nor with SP3 since day one it was released and installed. Few versions of BOClean changed since.