You need to change to Off Mode.  A mode change is required because Repelit protects against unwarranted installs by default.  

Double check your Automatic Update settings.  Do not use the setting “Automatically download the updates, and install them on the schedule that I specify”.

Repelit requires you to change to Off mode for operating system updates.  If you are not in front of your computer when the update tries to automatically install the patches, Repelit will remove items.  For this reason it is better to do the updates manually or download the updates manually and prompt for installation.  This will give you the opportunity to switch Repelit into Off mode when you are prompted to do the updates.  You can go ahead with the updates after Repelit is in Off mode.