Gradle presubmit not running all tests

For PR https://github.com/apache/beam/pull/4829

The following test failed (flakily) and succeeded on retry in Maven:

[https://builds.apache.org/job/beam_PreCommit_Java_MavenInstall/org.apache.beam$beam-runners-direct-java/18505/testReport/org.apache.beam.sdk.io/FileIOTest/testMatchWatchForNewFiles/](https://builds.apache.org/job/beam_PreCommit_Java_MavenInstall/org.apache.beam$beam-runners-direct-java/18505/testReport/org.apache.beam.sdk.io/FileIOTest/testMatchWatchForNewFiles/)

While investigating the original failure, I was unable to find it in the logs of the Gradle presubmit, making we worry that it may not be covering all tsets.

Imported from Jira [BEAM-3825](https://issues.apache.org/jira/browse/BEAM-3825). Original Jira may contain additional context.
Reported by: bchambers.