SharePoint alerts are sent multiple times

We have an issue with the built in SharePoint alerts. This is happening in multiple sites but i will focus on one particular site.

I created an alert on a document library. This alert is set to send immediately for all and any change. I made a change to document A. I get an alert immediately saying Document A was changed. It will have a modified time of for example, 1:02pm by User A.

5 minutes later and sometimes 10 minutes later I get another alert telling me that Document A was changed. The modified time and person who modified the document is still the same. 1:02pm and user A.

Any idea what would cause this. It doesn't happen in every site. I would think a setting with mail configuration would cause all alerts to send multiple times.

Could permissions to a specific site cause this? Perhaps one of the service accounts permissions were removed and now that service account can't flag an item as no longer 'new'. So the alert system still sees a new item and keeps sending an alert.

Thanks for any suggestions.

LSTalbot