If you are hitting the file attachment limits on your email server then you will need to contact your Email folks for an explanation. Pending on how they have things configured it may or maynot be possible for them to configure an exception for your large scanning jobs.
A simple work around would be to use the Scan to Folder option to scan your large attachments to a public network folder. When you are done then go out to that location, retrieve the job and delete it from the folder. Normal network folders should not have file attachment limits on them.