Hi Mark,
Last night I had a realization why it seems like an upgrade issue to you. You probably previously had put your theme.skin file in /App_Themes/default so it was working fine, but what you need to keep in mind is that when you upgrade it will overwrite that file again with the original theme.skin file that ships with mojoportal in the /App_Theme/default folder. So when you upgrade you either need to remove that file from the package before uploading the new version or be aware that you need to restore that file to App_Theme/default after each upgrade.
Best,
Joe