I found the problem and everything is fine now. Since we are running Http://mysite.company.com I had to also crawl sps3://mysite.company.com. Then did a full crawl and worked like a charm. Thanks for all the help though!!
Time to go back to Central Administration, and first look at your Search service application's management page. Click the Content Sources link on the left hand side, and open/edit your Local SharePoint Sites content source. In the Start Addresses section, you will see a box with entries similar to those below:
Notice the sps3: line. This is the protocol SharePoint uses to read profiles. (Note: It isn't a "protocol", per se. It just instructs SharePoint to call a specific web service hosted at that address.) If you ran the wizard to configure your service applications, it will be pointing at the original web application created by it. You'll need to change it to reflect your new profile web application, then save the changes to your content source definition. Also, if you deleted the original wizard-created web application (or aborted its creation), you'll need to delete the regular http: line referencing it.
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