Can you describe your build environment a little more? In order for Isolator to start or stop, particularly if linking with a coverage tool, you need to be an administrator. I've personally run into some crazy issues when I try to run certain builds on, say, Windows Server 2008 when I'm a non-admin user.
If you think that's the case, you may want to
check out this tool I wrote specifically for enabling Typemock to be configured as a non-admin user. Run it as an admin and give it the name of your build user's account.
Otherwise... if you can tell us more about your environment (OS, .NET version, Isolator version, etc.) we can probably help you out a little better.