Hey Revz, there has been a similar problem, something about cfpupdat.exe being corrupted or the wrong version. Its is discussed here https://forums.comodo.com/news-announcements-feedback-cis/comodo-internet-security-541898221355-released-t72243.0.html;msg517539#msg517539 Maybe it will help, im not sure.
Could you please go to Comodo Internet Security folder in Program Files and tell us which version of cfpupdat.exe is being reported. Right click/Properties/Details->Specifically the file and product version.
Something you could try is copy and replace the one in the folder with the one found in the Repair folder found in the CIS main folder.
Might be worth a shot.
If you are going to do a clean installation then don’t forget to export your active configuration and import it back in v 5.5. That will safe you from manually setting up CIS.