You could turn off the checkpoint that is generating the alerts, which is
probably in the Tools, real-time protection, application agent, view
application agents "tree."
However, I wouldn't want to do that without being sure that I understood
what was causing these alerts.
Have you scanned your system in safe mode? Can you find the text of such an
alert and post it here--one method might be: Tools, Real time protection,
view all blocked events.
Find one, highlight it, then click on the details pane on the right, and do
ctrl-a, ctrl-c to highlight and copy to the clipboard.
Post it here--let's see what is behind these alerts.