Filtering can result in what you describe.  You receive a new mail notification but the filter(s) moves the mail out of the new mail folder.  Do you have any new mail filters that are deleting messages or moving messages to a folder?  Is autofiltering enabled for one or more folders that is pulling mail out of the new mail folder?

After that occurrence of the 'Unknown' message with the very strange From and Subject fields and removal finally by deleting the *.CNM files.  Now I keep getting the New Mail Alert for one of my email addies and there are not any mail arriving.  It some times reports just one then maybe two up to maybe five new email without any shown nor any new moved to the SPAMHalter folder.  It looks as though there are ghosts arriving . . . this is getting a little spooky.

How many mail messages are in your new mail folder?

I have seen this on one staff member's account where I work and they had 1000's of messages in their new mail folder. They were using an old PC and it could not keep up with dynamically sorting the messages so that new messages appeared at the top of the list when they were delivered. Closing and opening Pegasus Mail was the only way to fix this (they have a shiny new computer now, so this has stopped happening).

[quote user="Greenman"]

How many mail messages are in your new mail folder?

I have seen this on one staff member's account where I work and they had 1000's of messages in their new mail folder. They were using an old PC and it could not keep up with dynamically sorting the messages so that new messages appeared at the top of the list when they were delivered. Closing and opening Pegasus Mail was the only way to fix this (they have a shiny new computer now, so this has stopped happening).

[/quote]

 Not in my PM any where near 1K maybe in a years time there may get close to that.  I keep my incoming mail box MT (empty) when mail comes in it is read deleted, forwarded, sorted to other boxes.  Never have I ever received mail at a rate higher than 35-40 with most of those being eaten by SPAMHalter.  I have three (3) accounts 1. My late Wife's; 2. one of mine, not used very much; 3. my primary account with my ISP.  The primary receives most of the mail, my secondary is the one that seems to be receiving the spook mail.  While typing this message the "Alert Window" popped up, I checked and there were only 5 messages, now it is MT again.  My system has been rebooted several times since this started, as you can tell it is still going on . .

 Ask David Harris if version five is ready, I am!!!!!