To reproduce the error, use the attached main.groovy script in a seed job with the Job DSL process to generate two jobs (example1, example2). Both jobs could be started on a windows environment and produce a 10 sec. sleep.

example2 is configured to be blocked when example1 is running. But both jobs can run in parallel as one can see in the attached BuildExecutorStatus.PNG

The config.xml of example2 has a entry for the plugin:
...
<properties>
<hudson.plugins.buildblocker.BuildBlockerProperty>
<useBuildBlocker>true</useBuildBlocker>
<blockingJobs>example1</blockingJobs>
<blockLevel>GLOBAL</blockLevel>
<scanQueueFor>DISABLED</scanQueueFor>
</hudson.plugins.buildblocker.BuildBlockerProperty>
</properties>
...

But the graphical view of example2 shows no selection for "Block build if certain jobs are running as shown in the attached example2_config.PNG