I wish I could help you, but I can't reproduce your problem.
Try the following:
1. Select Edit > Preferences > Open Preferences Location > plugins_prefs > EpubCheck
2. Open EpubCheck.json with a text editor, for example, Notepad or
Notepad++.
3. Insert the following line (marked in blue) at the beginning, before the first entry:
Code:
{
"debug": true,
"update_check": true,
and save EpubCheck.json.
4. Run EpubCheck, copy the complete output and paste it here.
Note that this change will actually cause the plugin to fail, but it should display additional information.