I'm sorry that you're running into issues with SiteImport. I know it doesn't help you, but I used SiteImport about 20 times today on various site while testing out some potential changes to better determine some specific types of links that users had reported issues with, and I never had an issue with JavaScript errors.
I'll assume that you have the latest version of the product installed at this point ( 3.0.1 )
If the product has never worked for you (going on 2 months+ based upon your post), then I suggest that you contact sales [at] webassist.com and ask for a refund.