Does this sound like what you are seeing?  From the help file:

The two colour buttons in this section allow you to alter the colours Pegasus Mail uses in its list of folders to identify folders that contain new mail. The first button, Colour for folders containing unread mail, defines the colour that is used for any folder containing messages that have not been marked as read. The second button, Colour for folders containing recent unread mail defines the colour Pegasus Mail should use to identify folders into which mail has been moved since they were last opened in the current session. Note that mail is only "recent" if it is received while the program is running: as soon as you exit and restart Pegasus Mail, any messages that were "recent" in the previous session simply become "unread" in the new session.

Notice that 1) "new mail" is not the same as unread mail, and 2) "new mail" is no longer considered new mail (recent) once in a new session of Pegasus Mail. 

Not sure if that's the proper terminology but ....

Our setup is with PMail configured Peg on my laptop being a 'server' and the wife's machine as a client (Pmail server configuration). I've set the options for her mail folders to change color when there's new mail. However when first launched, the folders don't show the specified color when there's new mail. Close and re-open and they're the right color. Using File/Read new mail doesn't force the color change either.

Not an earthshaking issue but one I'd like to sort out if possible since wife doesn't always notice the unread messages. I've pointed out that the message count to the right of each folder in the folder window will show x1:x2 where x1 is the total message count and x2 is the, or any, unread messages which is at least a help.

 Thanks for any suggestions.

I think you're probably way more competent than I am, but is this a mail filtering rule?  If so, is it set to filter when folder is opened or closed?