jenkins-job-builder doesn't filter when using template

I have a folder 'input' with two files in - emily.yaml and foo.yaml. I can generate a jenkins config for just the emily file without difficulty:

 jenkins-jobs --conf ~/devtools/jenkins-job-builder/etc/jenkins_jobs.ini-sample -l debug update input emily

It correctly skips foo. If I add template.yaml and change foo.yaml and emily.yaml to both use that template, and run the same command, it doesn't skip foo any more. I think it should. There could be an error in foo.yaml that I don't want to deal with right now. I do however want to get a new xml for emily.

Output when it works correctly:

$ jenkins-jobs --conf ~/devtools/jenkins-job-builder/etc/jenkins_jobs.ini-sample -l debug update input emily
DEBUG:root:Reading config from ~/devtools/jenkins-job-builder/etc/jenkins_jobs.ini-sample
DEBUG:root:Config: <ConfigParser.ConfigParser instance at 0x1400ea8>
INFO:root:Updating jobs in input (['emily'])
DEBUG:jenkins_jobs.builder:Parsing YAML file input/foo.yaml
DEBUG:jenkins_jobs.builder:Parsing YAML file input/emily.yaml
DEBUG:jenkins_jobs.builder:Ignoring job foo
DEBUG:jenkins_jobs.builder:XMLifying job 'emily'

Output when it works incorrectly:

$ jenkins-jobs --conf ~/devtools/jenkins-job-builder/etc/jenkins_jobs.ini-sample -l debug update input emily
DEBUG:root:Reading config from ~/devtools/jenkins-job-builder/etc/jenkins_jobs.ini-sample
DEBUG:root:Config: <ConfigParser.ConfigParser instance at 0x1506ea8>
INFO:root:Updating jobs in input (['emily'])
DEBUG:jenkins_jobs.builder:Parsing YAML file input/template.yaml
DEBUG:jenkins_jobs.builder:Parsing YAML file input/foo.yaml
DEBUG:jenkins_jobs.builder:Parsing YAML file input/emily.yaml
DEBUG:jenkins_jobs.builder:XMLifying project 'foo'
DEBUG:jenkins_jobs.builder:XMLifying project 'emily'

It should never have tried to do XMLifying project 'foo'