There are a couple possibilities here:
1. You are merging the JUnit results into the CC log file twice. Make sure you only have one <log> element with a <merge> of your JUnit results file.
2. You are running the tests twice - once directly from Ant and once from the CC build script. Make sure your build script isn't explicitly running the tests again after merging the results.
3. You have two projects configured in CC that are both running the same tests. Make sure each project is running unique tasks.
To troubleshoot, look at the build logs and CC log files to see if the tests are actually being run twice or if it is a merging issue. You may