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If you are using the Calibre viewer for an HTML fle, then it is worth realising that it first internally does a conversion to ePub for an file not already in epub format and then loads the result into the viewer. It could be something is affecting this conversion stage.
You could check this by doing an explicit conversion to ePub and then viewing the results. Having said that I am not sure that the viewer honors all the conversion options an explicit conversion does so you may get slightly different results.
Calibre's ebook viewer is not normally the best place to test an HTML file because of this underlying conversion. I always test the HTML in a browser and then do a conversion to ePub for loading into the calibre viewer.
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