Right, I was not very clear on what error was encountered. Sorry about that.
If CS5 is already running, then InDesign Server CS 5.5 won't start up because it complains that the instance is already in use. It says I need to run the multi-instance version.
If I stop the CS5 instance, then CS5.5 starts correctly. I'm not allowed to use the -instance switch because it is a single instance license key.
EDIT: I installed CS5 first.