Team City build failing almost as soon as git checkout starts with java.lang.NullPointerException

Question

My team city release build has randomly started failing. The only thing I can think of is a recent build of a different branch that was pushed as a release build. But we have done that before without problems.

I've tried cleaning the checkout directory before the build, still same issue.

Build log:

Build 'ProductName :: Release' #63
Started 'Mon May 30 23:40:30 AWST 2016' on 'DEFDEV' by 'admin'
Finished 'Mon May 30 23:40:31 AWST 2016' with status 'FAILURE Failed to start build'
TeamCity URL http://defdev.rdm.local:8081/viewLog.html?buildId=313&buildTypeId=ProductName_Release 
TeamCity server version is 9.1.6 (build 37459)

[23:40:23]i: TeamCity server version is 9.1.6 (build 37459)
[23:40:23]E: bt4 (7s)
[23:40:25] : Collecting changes in 1 VCS root (3s)
[23:40:25] :     [Collecting changes in 1 VCS root] VCS Root details
[23:40:25] :         [VCS Root details] "ProductName Tags" {instance id=9, parent internal id=3, parent id=ProductName_ProductNameTags, description: "git@bitbucket.org:ProductName/ProductName.git#refs/heads/master"}
[23:40:28]i:     [Collecting changes in 1 VCS root] Waiting for completion of current operations for the VCS root 'ProductName Tags'
[23:40:28]i:     [Collecting changes in 1 VCS root] Detecting changes in VCS root 'ProductName Tags' (used in 'Release')
[23:40:28]i:     [Collecting changes in 1 VCS root] Will collect changes for 'ProductName Tags' starting from revision 0d15ada28fe1b793fe88a070d7e69a53b0eb28c3
[23:40:30]i: Waiting for the agent to start the build
[23:40:30]i: Agent time zone: Australia/Perth
[23:40:30]i: Agent is running under JRE: 1.8.0_66-b17
[23:40:30]E: Unexpected error: java.lang.NullPointerException
[23:40:30]W: java.lang.NullPointerException
    at java.util.Objects.requireNonNull(Objects.java:203)
    at java.util.Arrays$ArrayList.<init>(Arrays.java:3813)
    at java.util.Arrays.asList(Arrays.java:3800)
    at jetbrains.buildServer.agent.impl.directories.DirectoryMapUnknownCleaner.removeUnknownToOld(DirectoryMapUnknownCleaner.java:51)
    at jetbrains.buildServer.agent.impl.directories.DirectoryMapUnknownCleaner.moveUnknown2Old(DirectoryMapUnknownCleaner.java:39)
    at jetbrains.buildServer.agent.impl.directories.DirectoryMapWatcher.prepareCleanupDirectory(DirectoryMapWatcher.java:39)
    at jetbrains.buildServer.agent.impl.directories.DirectoryMapWatcher.cleanupExpiredDirectoriesNow(DirectoryMapWatcher.java:44)
    at jetbrains.buildServer.agent.impl.buildStages.startStages.ClearExpiredBuildWorkingDirectoriesStage.doBuildStage(ClearExpiredBuildWorkingDirectoriesStage.java:29)
    at jetbrains.buildServer.agent.impl.buildStages.BuildStagesExecutor$1.callStage(BuildStagesExecutor.java:31)
    at jetbrains.buildServer.agent.impl.buildStages.BuildStagesExecutor$1.callStage(BuildStagesExecutor.java:24)
    at jetbrains.buildServer.agent.impl.buildStages.StagesExecutor.callRunStage(StagesExecutor.java:78)
    at jetbrains.buildServer.agent.impl.buildStages.StagesExecutor.doStages(StagesExecutor.java:37)
    at jetbrains.buildServer.agent.impl.buildStages.BuildStagesExecutor.doStages(BuildStagesExecutor.java:24)
    at jetbrains.buildServer.agent.impl.BuildRunActionImpl.doStages(BuildRunActionImpl.java:70)
    at jetbrains.buildServer.agent.impl.BuildRunActionImpl.runBuild(BuildRunActionImpl.java:50)
    at jetbrains.buildServer.agent.impl.BuildAgentImpl.doActualBuild(BuildAgentImpl.java:288)
    at jetbrains.buildServer.agent.impl.BuildAgentImpl.access$100(BuildAgentImpl.java:53)
    at jetbrains.buildServer.agent.impl.BuildAgentImpl$1.run(BuildAgentImpl.java:252)
    at java.lang.Thread.run(Thread.java:745)

[23:40:31]i: ##teamcity[buildStatisticValue key='buildStageDuration:buildFinishing' value='0.0']
[23:40:31] : Build failed to start. Artifacts will not be published for this build
[23:40:31]i: ##teamcity[buildStatisticValue key='buildStageDuration:artifactsPublishing' value='15.0']
[23:40:32] : Build finished