Reading back through our blog postings, we discovered the previous occurrence of the same issue back in December. The problem then was caused by deployment of XEP, and apparently it was triggered by confusion of two different versions of saxon.jar (or possibly two copies of the same version in different places). Worked with Greg on a plan to deal with this:

1. Try removing XEP from the existing deployment. If this solves the problem, then we approach the XEP tech support folks for more details on why it might be happening, and find another way to deploy XEP which doesn't screw up eXist. If that doesn't work, then:
2. Delete the existing Cocoon/eXist/XEP deployment completely, saving copies of our configuration files.
3. Unroll a new Cocoon/eXist war file in Tomcat, and install it with default configs. Test to check we can upload large files OK.
4. Restore our config files (not including XEP), and then test.
5. Attempt to reinstall XEP without triggering the problem again.

Meanwhile, work on EMLS and ScanCan2 is shelved; EMLS needs large file support, and ScanCan2 needs XEP, so neither will work until this is fixed.