I've been having this problem as well. I've tried adding "C:\Program Files\COMODO\*" and "C:\ProgramData\COMODO\*" to Shadow Defender's exclusion list, which keeps the files intact on the drive but continues to prompt me for definitions update on each boot. More than that, Comodo takes >30 seconds to enter any menu with updates done in this manner, whether it be the main control panel or advanced settings.
I have to do one of two things from there in order to restore Comodo to expected operation:
1) Select a different firewall configuration (being as my other ones have woefully outdated rulesets, I don't want to do this)
2) Reboot into Normal Mode and perform update from there.
Do I have to do this every time I want to update?