No real trick. The issue is probably that your JLinked application is set to use a URL of
www.site.com instead of site.com and you're going to the 'other' one. LinkedIn is very picky about the URLs you use in your application and what users actually visit.
If it works on
www.site.com and not site.com (or vice versa), try setting the "Javascript API Domain" option in your LinkedIn application to:
http://www.site.com, http://site.com
If that doesn't help, please post the URL of a problem page from your site so we can take a look.
Thanks,
Alex