Clover does not instrument groovy source files, (groovy-eclipse compiler) when located in src/main/groovy

When building a groovy project with maven, I am trying to get clover code coverage reports. With all source files in .java and in src/main/java, clover works fine. However, with all source files in .groovy and in src/main/groovy, clover can not instrument the files (clover2:instrument, or clover2:setup).

Everything that I can find is saying that clover versions after 3.1.3 support the maven groovy eclipse compiler (so long as the groovy files are located in src/main/groovy). See this ticket: https://jira.atlassian.com/browse/CLOV-1021?page=com.atlassian.jira.plugin.system.issuetabpanels:changehistory-tabpanel

There is another support ticket that I found that seems to cover the same issue, however I cannot access it. Here is the link
https://support.atlassian.com/browse/CLV-5878

A partial output log is included here. I will try to come up with a small test project that I can upload here. Any help would be appreciated.