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Go to Marketo Admin > Salesforce settings and check to make sure you're not getting a failed synch error. You will see the last synch date in the upper right of your screen.
That profile setting shouldn't mess up the synch. Could be a different underlying cause. It should only take a few minutes to synch between the two system but that time can vary.
The sync shouldn't take more than 30 minutes or so. Is it possible that the leads don't match because your validation rules are not met by the leads who havent synced over?
There are other anomolies that can occur on the SFDC side which could allow your sync to break as well, but checking the validation rules is usually a good starting point. Also, if anyone has changed a password, you will need to update your security token to re-enable the sync.
Doh, that was it!
Just out of curiosity, was it a password change, or the validation rules that were breaking the sync/causing the discrepency in lead counts between the two systems/programs?
Glad you were able to get it fixed :)