what i did to solve this
I have been having the same problem jconway1968 is having. I converted most of my ebooks in previous calibre versions, thus I used .36 or .37 for only a few. This led me to believe the issue was an isolated case. However, in .37 i tried converting a few pdfs that I knew had successfully been converted to epub in previous calibre versions and these presented the same issue. Thus i 'downgraded' to 0.6.31 and my conversions were then carried out flawlessly (i didn't enable anything in 'Look and Feel' besides the default font size key).
I just keep .31 installed on my XP partition for conversion purposes and use .37 on win7 for organizational purposes.
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