I have two workarounds for this. Since they are workarounds, they are of course not very good.
My understanding ( as a user ) is firstly that trashing is just a folder move to a folder called Trash.
Therefore, the problem as posted above also applies to moving a message between folders on the iPhone - the original message appears to linger in MobileMe.
Secondly, that an IMAP trashing consists of three steps: (a) COPY the message to Trash folder, (b) mark the original message for deletion, (c) 'expunge' the messages marked for deletion. Step (b) is a problem in MobileMe, since messages marked for deletion are not highlighted to the user in any way, so they look like they have not been processed. So, the trick is to convince MobileMe to do an EXPUNGE.
WORKAROUND 1
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This works for me directly in MobileMe: Move any message from the Inbox to another folder - causes MobileMe to expunge all messages-marked-for-deletion from the Inbox.
Say you have trashed ten messages from your iPhone Inbox. When you go to MobileMe, you will see the ten messages in the Trash folder (but you might not remember which ten). These are the MOVED messages. You also see the original ten messages still in the Inbox folder. These messages have indeed been marked for deletion (I can see that from from my sync'd Outlook2007), but MobileMe just isn't showing you that. If you move any message from the Inbox ( say, manually move one of your trashed messages to Trash ) all ten messages will disappear!
WORKAROUND 2
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If you have Outlook2007, you can force MobileMe to purge. In Outlook2007, select your me.com account, and then the inbox. You may see your marked-for-deletion-messages with a strikethrough and greyed out. Select Edit > Purge > Purge marked items in [email]xxxx@me.com[/email].
Alternatively, in Outlook2007, you can automate the purging slightly. Navigate to: Tools > Account Settings > (select your me.com account) > Change > More Settings > General. Check the checkbox 'Purge items when switching folders online'. Once you have done this, all you have to do is visit your Inbox from Outlook2007, then leave the folder or close Outlook and the purge will happen automatically.
I hope this helps some people. It certainly helps me, because I use my iPhone to classify my emails for actions as they come in. So now, by using these workarounds, MobileMe can catch up on what I have done.
Luck to all,
P.