In 9.3 there is a Popup Aggregation feature that shows only one popup if multiple incidents were generated in a short span of time.
Did you cross check whether there was an equal number of incidents in the Incident Manager?
Reg. the Outlook add-on issue, work with McAfee Support. Sounds like a bug to me.
Some file hosting solution normally check for the file hash prior to upload.
If you have to upload the same file , the actual POST activity does not happen hence you wont get the pop up.
Do a check with wireshark if this is the case for dropbox as well.
I trust you are using the Dropbox apps on your PC?