Did you ever find a solution to this? I have got the exact same problem upgrading from 6.13 to 6.2.
We have created a separate 'Update EEPC Themes' task, which updates only EEPC themes.
When rolling out a new version, we create a new theme, based on the existing theme for that version.
After rolling out, after the first reboot, the screen changes to the default McAfee one.
After the next reboot, the theme is changed back to ours.
Hope this helps.
Thanks mreco. I will try that.