Here's an open-source utility to help quickly create a proper ePub zip container from a folder.
To use, select your ePub "mimetype" file and choose a Filename.epub to save as. Then click the "Create ePub File" button.
All files inside the source folder will be included in the ePub file.
Installer with auto-updater:
setup.exe
Zip download with no installer:
ePubPack-1.3.2.0.zip
Site:
http://sourceforge.net/projects/epubpack/
License: GPL v3 or later
Requirements: Windows 7, Vista or XP &
.Net 4.0
Please let me know if there are any bugs.