I just installed 3.1.3 and upgraded from Bamboo 3.0.
I was working on a new script to take advantage of the Task system that was added in the new version.

It happens on an Ant task on the first stage of a build job.

On the Task Configuration dialog on the optional line for Environment Variables I specify a few custom environment variables and I also specify a custom Path variable to accomodate different build environments on different projects.

When I tell the plan to run it fails because some tools can't be found in the path. In the build log I can see that the "Path" variable has been set twice and it looks like the second time it's being set it's overwriting the custom path data I had specified.