There appears to be a conflict with the Seam multi-part filter and the rich:FileUpload which also uses a multipart filter. I got this to work. To be able to use both, I set a url-pattern in the components.xml for the Seam Filter that matches the pages (below) that the third party posts to. This also allows the rich:FileUpload to still work on other pages that don't match the pattern. Still not sure what changed with the upgrades that were made to the frameworks.
<web:multipart-filter create-temp-files="true" max-request-size="1000000" url-pattern="/EmailProcessing/*"/>