EMF resource load - SAXParser reading map twice - resources

Question

I'm having problems with persistence in EMF. The problem occurs when I add an element to a file that contains a map of elements. The process is:
Load file
Add element
Save file
The first time I add an element, it works fine. But if I try to add another, it reads
the list in twice before adding the new element. All subsequent uses also read the list twice.
EXAMPLE
I start with a file that looks like this:
<?xml version="1.0" encoding="ASCII"?>
<org.eclipse.mbt.core:CoreServicesResources xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:org.eclipse.mbt.core="http://org/eclipse/mbt/core">
<primaryResources>
<elementsMap key="1">
<value URI="1">
<traceabilityProperties traceable="true" derived="true" topLevel="true" />
<keywords tags="foo" />
</value>
</elementsMap>
</primaryResources>
</org.eclipse.mbt.core:CoreServicesResources>
If I add a new element, I end up with a file that looks like this, which is correct:
<?xml version="1.0" encoding="ASCII"?>
<org.eclipse.mbt.core:CoreServicesResources xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:org.eclipse.mbt.core="http://org/eclipse/mbt/core">
<primaryResources>
<elementsMap key="1">
<value URI="1">
<traceabilityProperties traceable="true" derived="true" topLevel="true"/>
<keywords tags="foo"/>
</value>
</elementsMap>
<elementsMap key="2">
<value URI="2">
<traceabilityProperties traceable="true" derived="true" topLevel="true"/>
<keywords tags="bar"/>
</value>
</elementsMap>
</primaryResources>
</org.eclipse.mbt.core:CoreServicesResources>
However, if I then add another element, I get this, which is incorrect:
<?xml version="1.0" encoding="ASCII"?>
<org.eclipse.mbt.core:CoreServicesResources xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:org.eclipse.mbt.core="http://org/eclipse/mbt/core">
<primaryResources>
<elementsMap key="1">
<value URI="1">
<traceabilityProperties traceable="true" derived="true" topLevel="true"/>
<keywords tags="foo"/>
</value>
</elementsMap>
<elementsMap key="2">
<value URI="2">
<traceabilityProperties traceable="true" derived="true" topLevel="true"/>
<keywords tags="bar"/>
</value>
</elementsMap>
<elementsMap key="1">
<value URI="1">
<traceabilityProperties traceable="true" derived="true" topLevel="true"/>
<keywords tags="bar"/>
</value>
</elementsMap>
<elementsMap key="2">
<value URI="2">
<traceabilityProperties traceable="true" derived="true" topLevel="true"/>
<keywords tags="foo"/>
</value>
</elementsMap>
<elementsMap key="3">
<value URI="3">
<traceabilityProperties traceable="true" derived="true" topLevel="true"/>
<keywords tags="bar"/>
</value>
</elementsMap>
</primaryResources>
</org.eclipse.mbt.core:CoreServicesResources>
When I debug the code, the problem seems to be happening somewhere in the parser. I'm using the Java SE-11 System library, and the parser is com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
Has anyone else had problems like this?