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Calibre does not have a PDF reader - ony a Calibre EPUB viewer!
In the a calibre preferences you can tell Calibre to use either it's internal viewer or the system viewer for each file type. If you tell calibre to use it's own viewer then any book not already in ePub format is internally converted to ePub before viewing. As conversions from PDF tend to to work well the default setting in calibre is to use the system PDF viewer for PDF files.
My guess is that calibre is set to use the system PDF viewer and installing the PDF software changed the system level settings for PDF viewing. Therefore to get back the old behaviour you need to reset your settings for the system PDF viewer (which were probably set to something like Acrobat Reader).
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