1. Created a trunk project in Jenkins and verified that it built successfully.
2. Created a feature project through Jenkins
3. Attempted to build the branch only to find that Jenkins couldn't locate the necessary batch files.

Upon further investigation I noticed that Jenkins was checking out the files to a subdirectory (same name as branch) of the workspace instead of directly to the workspace folder like the trunk was doing. That's when I realized the the "Local module directory (optional)" setting for the branch didn't match the trunk. The trunk's option was set to '.', but the branch's option was empty. In order for a branch to build straightaway this setting should be copied from the trunk project.