Its hard to resolve without having the original PDF, as you know PDF is a 'pig' to convert. FWIW I am not aware of anything in calibre's PDF converter that could cause this problem - but I don't use it that much.
If you use Windows you could try the MobiPocket Creator tool (there's a link in PDF Conversion sticky) to create HTML or PRC, and convert that to EPUB and look at in editor (and Sigil for a 2nd opinion if you're inclined).
If the PDF is
not copyright protected you could post it here and I'll see if I can work it out. Or you could attach it to a Bug Report here ==>>
Bugs : calibre and mark it
Private and perhaps a developer can help.
BR