'It appears there is a hidden script somewhere that is being triggered?' - if a statement - it is incorrect; if a question - no there is not any hidden script(s).
Try the following:
Go to '~/Library/Mail/POP-x/INBOX.mbox/Messages/' folder (where 'x', in 'POP-x', is the troubled e-Mail account) and locate, trash (in the 'Dock' trash can), and delete - the problematic e-Mail's '.emix' file (just double click on - to open, view, and close each '.emix' file, at a time, to locate the problematic e-Mail message).
Return to 'Mail's 'Message Viewer's window to delete (do a right button click [or '<control> click'] 'Delete' menu item selection) the now deleted problematic e-Mail's listing.
Finally, select 'Mail's 'Mailbox, Erase Delete Messages, In All Accounts' ('Command K') sub-menu item.
