I have a federation trust setup on a 2008 R2 server. The initial site is reached through the https://adfs.domain.com/adfs/ls/idpinitiatedsignon.aspx?wa=wsignin1.0
but when you click the button you end up with
https://srvr2008.domain.local/adfs/ls/IdpInitiatedSignon.aspx
how can i change it from the computer name back to the domain name.
This may well be a DNS or load balancer issue.
ADFS needs a federated service name and you can change it in the ADFS "Edit federation service properties" via the wizard.
Note that this should reflect to the SSL certificate name and the DNS.