Which browser do you use for access? If it is Internet Explorer, try Mozilla Firefox. See if the problem goes away. It seems to have made a good work around of the problem for many other people. Also does this only happen within the local network or via the internet aswell? As most people with this problem find it is only within the local network. If it is only within the local network, try access from a wireless networked computer rather than a wired network. As these issues within the local network for others seem to be related to computers connected via ethernet cable. Thirdly have you installed SCOM R2 agent? If so you may want to uncheck client authentication on the SCOM certificate. As this also slows down login. However this will prevent SCOM from communicating with ISA servers.
Many people have gotten around most of these issues with a simple update. So that would be my first port of call.