I have the FCS client working on ISA 2006 servers make sure as chrisw_uk mentions on port 5723 also make sure to check if your port is still set on this default. Create the ISA rule to allow this port into your ISA.
Also have you installed the Forefront Security Console?? Check your MOM server to update attributes..
Maybe your WSUS is missing a required update, check the Microsoft Catalogue and download the required Forefront Updates and Clients updates, if all fails just install manually install on your isa 2006 systems.
Mark Norman, Praxa