There is an important difference in the web server connector on Windows (wsconfig.exe) on ColdFusion 10 which of course moved ColdFusion as a Java Application Server from JRun to Tomcat as the Servelet Container.  This applies to multiple instance installs.

On ColdFusion 9 and prior there was one wsconfig.exe utility only which lived in {drive}\JRun4\bin.  In ColdFusion 10 the first main difference is the directory structure which changed very much for the better in my opinion, now every install has the same directory structure starting in {drive}\ColdFusion10.  All instances you add will be under this root and the parent folder for each instance will be in the ColdFusion10 root and have the same name as the instance, so if you add an "instance_01" it will show up as {drive}\ColdFusion10\instance_01.  Here is the main point relating to wsconfig.exe each instance you add has its own copy which you should use to connect ColdFusion10 to web sites it is located in...

{drive}\ColdFusion10\instance_01\runtime\bin.

If you use the one installed when you install ColdFusion10, located in Start > Programs you can get unpredictable results.