Steps to reproduce (NB 6.5 RC2 used):

1) Create directory c:/tmp/groovyt, add simple GroovyTest.groovy file into this directory. Content of the file:

class GroovyTest {
    static void main(String[] args) {
        println "GroovyTest"
    }
}

2) Start NB 6.5 RC2

3) create new java project (Java Application) named "groovyt", 
uncheck "Create Main Class", press Finish

4) Select Project properties, go to Build/Groovy, check "Enable Groovy"

5) Select Project properties, go to Sources , remove default "src" entry, 
press "add Folder", select (add) c:/tmp/groovyt

6) Clean and Build project -> error occurs telling that srcdir does not exist:
"C:\...\groovy-build.xml:16: srcdir "C:\...\groovyt\${src.dir}" does not exist!"

(Note: I had replaced the full path with "...")

In case groovy sources are placed into default src directory, 
program can be compiled and run correctly.