Using the following example build script:

apply plugin: 'groovy'

repositories {
	mavenCentral()
}

dependencies {
	groovy 'org.codehaus.groovy:groovy:1.8.0'
	compile 'commons-cli:commons-cli:1.1'
}

Groovy 1.8.0 uses Commons CLI 1.2 [1], but if you specify that your project contains a user-defined compile dependency on Commons CLI 1.1 (as I do above), then version 1.1 gets used not only on the compile classpath, but also on the Groovy compilation classpath. So e.g. if you run "gradle compileGroovy --debug", here is an example of the log of the (erroneous) command line used:

12:44:06.130 [DEBUG] [org.gradle.api.internal.project.ant.AntLoggingAdapter] Execute:Java13CommandLauncher: Executing 'C:\Program Files\Java\jdk1.5.0_09\jre\bin\java' with arguments:
'-classpath'
'C:\Documents and Settings\dgredler\.gradle\cache\commons-cli\commons-cli\jars\commons-cli-1.1.jar;C:\Documents and Settings\dgredler\.gradle\cache\org.codehaus.groovy\groovy\jars\groovy-1.8.0.jar;C:\Documents and Settings\dgredler\.gradle\cache\antlr\antlr\jars\antlr-2.7.7.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm\jars\asm-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-commons\jars\asm-commons-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-tree\jars\asm-tree-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-util\jars\asm-util-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-analysis\jars\asm-analysis-3.2.jar;C:\java\gradle-1.0-milestone-2\lib\commons-cli-1.2.jar'
'-Dfile.encoding=Cp1252'
'org.codehaus.groovy.tools.FileSystemCompiler'
'--classpath'
'C:\Documents and Settings\dgredler\.gradle\cache\commons-cli\commons-cli\jars\commons-cli-1.1.jar;C:\Documents and Settings\dgredler\.gradle\cache\org.codehaus.groovy\groovy\jars\groovy-1.8.0.jar;C:\Documents and Settings\dgredler\.gradle\cache\antlr\antlr\jars\antlr-2.7.7.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm\jars\asm-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-commons\jars\asm-commons-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-tree\jars\asm-tree-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-util\jars\asm-util-3.2.jar;C:\Documents and Settings\dgredler\.gradle\cache\asm\asm-analysis\jars\asm-analysis-3.2.jar;C:\java\gradle-1.0-milestone-2\lib\commons-cli-1.2.jar'
'-j'
'-Fg'
'-Jsource=1.5'
'-Jtarget=1.5'
'-d'
'C:\work\trunk\Core\r2\Development\Sources\xbo\test\build\classes\main'
'C:\work\trunk\Core\r2\Development\Sources\xbo\test\src\main\groovy\Test.java'

As you can see, there are two classpaths: the run classpath used to run the FileSystemCompiler class, and the compile classpath. Both of these classpaths contain two versions of Commons CLI: version 1.2 included with Gradle, and version 1.1 specified by the user as a compile dependency. In my opinion the run classpath above should contain only Gradle's version of CLI, whereas the compile classpath should contain only the user-specified version of CLI, not Gradle's version.

[1] https://svn.codehaus.org/groovy/tags/GROOVY_1_8_0/build.gradle