This was tested on a Windows 2003 server. The issue was, when the server was rebooted, the ISA services had to be manually started and would not start automatically.

The fix:

1) Click Start
2) Click run
3) Type regedit and click OK. (Ensure you have a backup)
4) Navigate to KEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control
5) Right click and create a new DWORD key
6) Name the DWORD key ServicesPipeTimeout
7) Click decimal and type value of 60000 (This is 60 seconds)
8.) Reboot the server and services should start automatically