I doubt that anyone here is familiar with the exact setup you describe. However, that's probably not that important. In cases like these what's usually important is the served page. After all, that's what the browser must contend with. Now, it sounds to me as though, if all of what you say is true, that there is some typo (most likely) or something that is disabling the main stylesheet. To get a better idea though, I would need to see the page.
Please post a link to the page on your site that contains the problematic code so we can check it out.
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