Found out a little more. The GIS Server appears to be running Tomcat as its web server. There is a crossdomain.xml file at its root. According to the documentation, this is open automatically (see below). I am still confused on why FlashBuilder is giving me this error then. Anybody have any ideas on this? Thanks!
-From help
"By default, ArcGIS Server allows cross-domain requests. A set of client access policy files are placed on your GIS server for this purpose when you install ArcGIS Server. These should not be removed, opened, or modified."