Another thought. Considering the way that the 2.0.0 release is structured, it looks like the Kobo side of the internal disk is not cleared before installing the new firmware. Otherwise, why would there need to be a Qt 4.6.2 directory, as it would just get replaced by the 4.8.0 directory.
This would explain why the fonts differ. Times New Roman in not in the 2.0.0 release. So, if it wasn't already on your Kobo, it won't be installed. But, if it was installed on a previous release, then it will not be deleted when the new firmware is installed, and the font will be available.
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