Andrew,
If you are using AutoCad I would sincerely recommend upgrading to Pro. Acrobat Pro has a toolbar similar to Word/Excel, etc. to aid in the conversion of the CAD information.
As for your conversion process.. let me guess... File | Print --> Adobe PDF printer? That performs a CAD --> PostScript --> PDF transform. Depending on how the objects are described when coming out of the CAD system (e.g. arcs vs. line segments) can have a major impact on the resulting PDF.
As mentioned before - side-by-side comparison of versions, steps, and settings will be the key to figuring this out. Click on all the properties and settings buttons and tabs you can find.
It's in there... computers aren't that smart yet. They are still pretty deterministic.
Thanks.
Doug