Within the main.inc.php file i've configured that the default folders must be created.
To these default folders belongs also the Trash folder.
I think the "mark as deleted" is only usefull when you don't have a Trash folder.
Otherwise, the behaviour looks a little weird indeed, but not buggy i think.
Within the RC config file main.inc.php, you should play with these settings to get the result you want:
// move messages to this folder when deleting them
// leave blank if they should be deleted directly
$rcmail_config['trash_mbox'] = 'Trash';
// Set TRUE if deleted messages should not be displayed
// This will make the application run slower
$rcmail_config['skip_deleted'] = FALSE;
// Set true to Mark deleted messages as read as well as deleted
// False means that a message's read status is not affected by marking it as deleted
$rcmail_config['read_when_deleted'] = TRUE;
// When a Trash folder is not present and a message is deleted, flag
// the message for deletion rather than deleting it immediately. Setting this to
// false causes deleted messages to be permanantly removed if there is no Trash folder
$rcmail_config['flag_for_deletion'] = FALSE;
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