@RbnJrg: I've tested the plugin with many ePub2 files and never had any validation problems with the generated ePub3 files.
The only message that I consistently got is:
External DTD entities are not allowed. Remove the DOCTYPE.
However, this is a known bug in epubcheck 3.0.1 related to the .ncx file.
As for ADE 4. They released a new version with MathML support some time ago. If you haven't already installed it, re-check your file with the latest version. For good measure also check the converted ePub3 file with
Readium.
Please also post an ePub2 test file with svg images for KevinH.