Threepress has contributed patches to a number of significant bugs and improvements to epubcheck recently:
Error message generated for valid ISO8601 date [BUG]
Checking for unused files which are not in the manifest [ENHANCEMENT]
Existence of files referenced in guide not checked [BUG]
Version r128 has broken test suite [BUG]
The unmanifested file warning in particular has been a critical issue for publishers working in the EPUB ecosystem, and we believe this update alone warrants a new public release and a version number push. The date issue has also been problematic for EPUB files generated out of tools like Calibre that produce dates with timestamps in them.
Download epubcheck 1.1-rc1: epubcheck-1.1-rc1.jar. Note that you will need to know how to run the command-line epubcheck for this, and is intended for developers only.
Please report all issues to the epubcheck issues list, not this blog.