Hello jaythom and welcome to BC
You did the right thing. Frequently security programs will flag files from specialized cleaning tools, because the same programming that allows these to work also allows malware to work, rather like the knife that a surgeon can use to help heal someone, or that someone else may do mayhem with. I'd go ahead and uninstall and delete SmitFraudFix now that you have finished using the removal guide.
As for the other issue, no one security program finds everything, just as no library has every book. This doesn't make one better or worse than the other, it just means that while you generally use one, you pay a visit others to fill in the gaps as it were.
I'd post a new topic in the Infected forum and paste in the complete online Symantec scan, and in the title mention a few of the files it finds.