Mail rebuild mailbox issue with Gmail

I set up Mail 4.6 to receive and send e-mails to and from Gmail as per the instructions on the Gmail site and used additional information on this forum.
What is happening is whenever I rebuild the gmail folder it downloads again all the files I have deleated. I rebuild after deleting a lot of Spam and e-mails I no longer need.
As recommended the account is set as a imap account.
Under the mailbox tab it is set:
DRAFTS: Store draft messages on server - box not checked
SENT: Store sent messages on server - box not checked
           Delete message: dropdown set to: One day old
JUNK: Store Junk messages on server - box not checked
          Delete message: dropdown set to: One day old
TRASH: Move deleted message to the Trash mailbox - box is checked
             Store deleted messages on the server:  - box not checked
             Permanently erase Delete message when: dropdown set to: One day old
Under the Advance tab it is set:
Enable this account - box is checked
Include when automatically checking for new messages - box is checked
Compact mailboxes Automatically - is greyed out - box is checked
Keep copies of messages for offline viewing: dropdown set to: All messages and their attachments
I am not sure is this last item of  'Keep copies of messages for offline viewing' refers to the the Gmail server or the mail box - if it is the gmail server then I guess Mail is just syncronising with this; thus any mails I delete will be down loaded again. ((All the other mail servers I use I set under Advance tab to 'Remove copy from server after retrieving message' - but this option is not shown for gmail.
Two things are happening:
a) When I delete files in the Mail, Gmail folder the next time I rebuild the mail box I get 1000 + emails down loaded; even though I may only have deleted 30 or so.
b) At other time mail will show downloading e-mails in the blue download indicator, but no new emails appear.
Would welcome some direction on how to resolve these issues; thank you.

The issue with g-mail became cronic. Now I can't delete e-mails received to my gmail account.
When I try to delete emails in the gMail or Mail inbox the following message is show.
The Message could not be removed to the mailbox (null)
The destination mailbox "(null)" does not allow messages to be moved to it.
This started after following the recomendation I found in the forum to sync gmail folders to the Mail - folders.
I am looking for solution to get back to the original condition that while not what it should be it is better than now.
Was hoping for solution were I wouldn't have to delete gmail account from mail then start again.
Any ideas welcome as I would like to delete emails in the gmail folders in Gmail without logging into Gmail every time.
Thank you

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