Originally Posted by NLight95
Is it because it's not formatted for e-book devices and there are many text reflow issues?
I'm thinking about converting any PDFs I have over to ePub.
Exactly correct. Your format of choice is ePUB and Calibre will convert to that very well for you.
However PDF to any format is often hit and miss. I would recommend opening up the PDF files that are proving difficult to convert in Calibre into Mobipocket Creator and convert to MOBI. Then Calibre can do the final conversion to ePUB. I use this often when converting stubborn PDF's.
In the main though, Calibre converts PDF's to true ebook formats very well indeed.