I came across a situation where I had to create an SSO solution in UAG between trunks.  I followed the links below but I made sure that I matched the 'Domain' field in each WhlFiltSSO.ini file and <trunkname>sso.inc.

After making these changes I reset IIS and then I could navigate between URL's beteeen trunks.

http://blogs.technet.com/b/edgeaccessblog/archive/2010/04/14/forefront-uag-and-adfs-better-together.aspx

http://technet.microsoft.com/en-us/library/ee921441.aspx