Pentaho Kettle/PDI fails on second request - pentaho

Question

I have the latest version of Kettle/PDI. Carte is running locally on Windows with the following configuration:
<slave_config>
<slaveserver>
<name>master1</name>
<hostname>localhost</hostname>
<port>8081</port>
<master>Y</master>
</slaveserver>
<repository>
<name>PDI Repo</name>
<username>username</username>
<password>password</password>
</repository>
</slave_config>
And in .kettle/repositories.xml:
<repositories>
<connection>
<name>PDI Repo</name>
<server>127.0.0.1</server>
<type>MYSQL</type>
<access>Native</access>
<database>pdi</database>
<port>3306</port>
<username>username</username>
<password>Encrypted password</password>
<servername/>
<data_tablespace/>
<index_tablespace/>
<attributes>
<attribute><code>EXTRA_OPTION_MYSQL.defaultFetchSize</code><attribute>500</attribute></attribute>
<attribute><code>EXTRA_OPTION_MYSQL.useCursorFetch</code><attribute>true</attribute></attribute>
<attribute><code>FORCE_IDENTIFIERS_TO_LOWERCASE</code><attribute>N</attribute></attribute>
<attribute><code>FORCE_IDENTIFIERS_TO_UPPERCASE</code><attribute>N</attribute></attribute>
<attribute><code>IS_CLUSTERED</code><attribute>N</attribute></attribute>
<attribute><code>PORT_NUMBER</code><attribute>3306</attribute></attribute>
<attribute><code>PRESERVE_RESERVED_WORD_CASE</code><attribute>N</attribute></attribute>
<attribute><code>QUOTE_ALL_FIELDS</code><attribute>N</attribute></attribute>
<attribute><code>STREAM_RESULTS</code><attribute>Y</attribute></attribute>
<attribute><code>SUPPORTS_BOOLEAN_DATA_TYPE</code><attribute>Y</attribute></attribute>
<attribute><code>SUPPORTS_TIMESTAMP_DATA_TYPE</code><attribute>Y</attribute></attribute>
<attribute><code>USE_POOLING</code><attribute>N</attribute></attribute>
</attributes>
</connection>
<repository>
<id>KettleDatabaseRepository</id>
<name>PDI Repo</name>
<description>PDI Repo</description>
<connection>PDI Repo</connection>
</repository>
</repositories>
You'll notice these are pretty much the default with some specific configuration for the repository database. Through Spoon, I've created a simple transformation that runs a select on a database table, performs some simple calculations on the columns, and returns some JSON.
If I tell the transformation to run on master1, it works and spits out the JSON.
If I run exactly the same command again, it errors:
2016/01/29 10:05:53 - PDI Repo - ERROR (version 6.0.1.0-386, build 1 from 2015-12-03 11.37.25 by buildguy) : Error disconnecting from database :
2016/01/29 10:05:53 - PDI Repo - Unable to commit repository connection
2016/01/29 10:05:53 - PDI Repo -
2016/01/29 10:05:53 - PDI Repo - Error comitting connection
2016/01/29 10:05:53 - PDI Repo - at java.lang.Thread.run (Thread.java:745)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.trans.step.RunThread.run (RunThread.java:121)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.trans.step.BaseStep.markStop (BaseStep.java:2992)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.trans.Trans$1.stepFinished (Trans.java:1233)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.trans.Trans.fireTransFinishedListeners (Trans.java:1478)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.www.BaseJobServlet$3.transFinished (BaseJobServlet.java:170)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.repository.kdr.KettleDatabaseRepository.disconnect (KettleDatabaseRepository.java:1655)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.repository.kdr.delegates.KettleDatabaseRepositoryConnectionDelegate.disconnect(KettleDatabaseRepositoryConnectionDelegate.java:257)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.repository.kdr.delegates.KettleDatabaseRepositoryConnectionDelegate.commit(KettleDatabaseRepositoryConnectionDelegate.java:283)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.core.database.Database.commit (Database.java:738)
2016/01/29 10:05:53 - PDI Repo - at org.pentaho.di.core.database.Database.commit (Database.java:757)
I don't understand why the connection to the repository database fails after the first request. Carte continues to run, despite this error, but will throw errors like this when accessed via URL:
<webresult>
<result>ERROR</result>
<message>Unexpected error executing the transformation:
java.lang.NullPointerException
at org.pentaho.di.core.vfs.KettleVFS.getFileObject(KettleVFS.java:128)
at org.pentaho.di.core.vfs.KettleVFS.getFileObject(KettleVFS.java:106)
at org.pentaho.di.trans.TransMeta.<init>(TransMeta.java:2716)
at org.pentaho.di.trans.TransMeta.<init>(TransMeta.java:2684)
at org.pentaho.di.trans.TransMeta.<init>(TransMeta.java:2661)
at org.pentaho.di.trans.TransMeta.<init>(TransMeta.java:2641)
at org.pentaho.di.trans.TransMeta.<init>(TransMeta.java:2606)
at org.pentaho.di.trans.TransMeta.<init>(TransMeta.java:2569)
at org.pentaho.di.www.ExecuteTransServlet.loadTransformation(ExecuteTransServlet.java:316)
at org.pentaho.di.www.ExecuteTransServlet.doGet(ExecuteTransServlet.java:232)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:668)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:770)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:229)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255)
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:522)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
at org.eclipse.jetty.server.BlockingHttpConnection.handleRequest(BlockingHttpConnection.java:53)
at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:971)
at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1033)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:644)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
at org.eclipse.jetty.server.BlockingHttpConnection.handle(BlockingHttpConnection.java:72)
at org.eclipse.jetty.server.bio.SocketConnector$ConnectorEndPoint.run(SocketConnector.java:264)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:745)</message>
<id />
</webresult>
I dug through the code for that stack trace, and that means the Repository object is null. So, for some reason, Carte can connect to the PDI repository, but when it succeeds once, something errors and it drops the connection and can no longer find the transformations.