While writing the site monitor code, I decided to pass some control variables to the test cases using java system properties. I edited the ant junit task and set clonevm="true".
Apparently, this broke the dir property that was also passing into the junit tests. I noted (after many hours of wondering "heh, it was working before") that the "dir" will not take effect if you set clonevm to true. It seems clonevm also clones the current directory property.
It might be a good idea for junit task to still honour the dir property even if clonevm is true.