Discrepancy Between Mobile Me Folders and Mail Folders on iMac

Hi there,
When I use Mail 4.2 and check the number of messages in a folder I see a different number from what displays when I log in on the web at www.me.com.
I checked under Library\Mail and my account for some folders and the Messages folder under a specific mailbox does not display any messages either. Therefore, it seems that the Mobile Me web mail is not giving a true representation.
I have also noticed that my Sync settings for Mobile Me keep getting unchecked when I look at those settings. I have to re-enable this on a regular basis. Could this have anything to do with my problem? I think this started after I enabled my Google account to sync with my address book and also iCal.
I have tried syncing and have no problems so I am not sure what else to check. I suspect that there are messages in folders that Mail is not able to access which is puzzling.
Ideas and suggestions as to how to proceed to reclaim the messages in Mail would be much appreciated. One folder in particular has almost 1 GB of data that is not showing up on Mail but when you open that same folder on webmail it is not displaying messages there either but I think they're present because I'm missing a large amount of e-mail.
Thanks in hopeful anticipation as to how to resolve this.
Lynn

As I said I thought I had solved this problem, but apparently I still have this situation. If I set up my .Mac mail account in a Mozilla application I see not only the current folders but also the names of any previous folders that were used on .Mac. I know the profile in Mozilla is not the issue, it's the .Mac account. Therefore, how can all these old folders on .Mac be permanently removed? They must be hiding somewhere on the server but how would this be tracked down? Would it have to be done by Apple? I'm talking about 25 folders that are affected, i.e., no longer used or resident on the account.
Any suggestions would be much appreciated.
Lynn

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