I am using the Second Edition build, and when using the .NET Framework 2.0 template the version checking was not working. I inserted the following code to check the result:
Get File Version $WINSYSDIR$\\mscoree.dll into Variable MSCOREVER
What I got back was 0.0.0.0
However, if I change it to a hard coded path:
Get File Version c:\\windows\\system32\\mscoree.dll into Variable MSCOREVER
Please make sure $WINSYSDIR$ is initialized beforehand.
Easiest way: search for WINSYSDIR in the script (type CTRL+F and type in WINSYSDIR), then copy-paste the line that initializes it right above your call for the runtime.
Note: The sample script already performs this initialization for you. Please double-check that you did not accidentally delete the code (or are overwriting the variable later on).