I believe you are having issues related to SPR-11373. Specifically, the servlet specification is not clear on what should happen when performing multipart resolution within a Filter.
Have you tried using commons-fileupload instead? This is likely your best option. First add the following dependency:
<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>1.2.2</version>
</dependency>
Next ensure you have the following bean definition in your root application context.
<bean id="filterMultipartResolver" class="org.springframework.web.multipart.commons.CommonsMultipartResolver">
<property name="maxUploadSize" value="100000000"/>
</bean>
You can find a complete working example with both commons-upload (prefer this solution) and using tomcat using allowCasualMultipartParsing on SEC-2471