Don't know that I've run into your specific problem, but I've run into some confusion regarding why I was setting one limit but I was experiencing another. A couple things to make sure you're considering are:
zimbraMailContentMaxSize
zimbraFileUploadMaxSize
zimbraMtaMaxMessageSize
And whether you've reset the zimbra services.

(Sorry, the helpdesk technician aura took over me for a bit there).
Good luck!