Update to EPUBCheck
The IDPF released a new version of EPUBCheck, their EPUB validation tool. This version continues to validate both EPUB 2.0.1 and EPUB 3.0. The new verison is 3.0-RC-1. You can download the code.google.com here. I have also uploaded the file to the EPUBSecrets Dropbox here.
Make sure you keep your EPUB tools current, especially as it looks like there may finally be some movement toward retailer support of EPUB 3.