A few suggestions:
- Save the page as a webarchive,
in addition to a PDF.
- Try iCab for making PDFs
Bonus suggestion: check what you saved before you leave the page you want to save.
Btw, I take it you've restarted your Mac, or quit and reloaded Safari after previous attempts, and that this made no difference? Likewise, the same sites/pages consistently mess up this way?
Btw2, if you resort to screen captures, use a utility that saves the
entire page/frame, including the areas you may have to scroll to on screen.