This is probably because of an installed program that is configured to update at startup. Click on Start button , type "msconfig" without the quotes, then click on Startup tab. Disable everything, then restart. If the alert does not reappear, reenable the startup items one by one till the alert reappears. The item you enabled last would be the culprit.
When you say you've turned off updates, which updates did you mean? There can be windows updates, AV updates, Google updater updates, Adobe updates etc. etc.