OK, that explains it! It is an odd thing in Mail that when not selected to Move Deleted Messages to another folder, it affects more than deleted messages. It also affects email you manually mark as Junk, and also messages you are moving.
With deleted messages, when not selected to move them to another folder, they remain in the original mailbox (Inbox if that is where working). Then if you click on View in the menubar you will see either Show Deleted Messages, or Hide Deleted Messages. If your says Show, then you should click to see how many messages you deleted that are remaining in the mailbox but have been Hidden. Any deleted messages remaining in the mailbox can be Erased by clicking Mailbox in the menubar, choosing Erase Deleted Messages, which then should offer the choice of In the Selected Mailbox, which if clicked will Erase those messages.
What then is odd in Mail, is that this selection also results in Junk messages manually marked (but not those Automatically marked by the Junk Filter) moving to the Junk mailbox (assuming you have selected to have one), but also remaining in the original mailbox but Gray. The same occurs with moving messages -- they move but also stay in the origin mailbox, but Gray. Both of these residual messages can be removed using the same Erase Deleted Messages/In the Selected Mailbox.
Hope that is clear. If you change to have Deleted Messages moved to another folder (the Trash) then the operation of Junk and moved messages will be as you originally expected.
Ernie
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