I use Inkscape rather than Illustrator (mostly because as Inkscape is open source, most folks use it) and I normally don’t use parts editor because I find it easier to edit the fzp file directly. If I don’t have a suitable part I usually use a generic IC of the appropriate number of pins (because its svgs are the correct scale from Fritzing) or a generic header (whose scale is not correct) if it is an odd number of pins. In both cases the part factory will generate the pins with the correct sequence, it is only parts editor which will generate missing pins as far as I know. Illustrator may not be happy with something Inkscape did to the svgs, although I don’t know what exactly.
Peter