Are you using ADE on Windows or Mac??
MathMl is supported on ADE 4.0.3
I am using ADE 4.0.3 for Windows which states in the release notes:
Changes in ADE 4.0.3
MathML support is now available for ADE on Windows.
Here is a link to my test ePub that works on Apple iBooks reader, Readium app for Chrome, and Calibre ePub reader, but NOT on ADE 4.0.3
Please let me know if you can get it to work on your copy of ADE 4.0.3 for Windows
One would think that Adobe would provide at least one test ePub containing MathML equations as proof that ADE 4.0.3 does indeed support MathML.