Tested with JBoss Dev Studio Version: 2.0.0.CR1, Build id: R200812221144

Steps to repro:

1. Install JBDS.
2. download http://www.jboss.org/downloading/?projectId=jbossjbpm&url=http://downloads.sourceforge.net/jbpm/jbpm-installer-3.3.0.GA.jar
3. `java -jar jbpm-installer-3.3.0.GA.jar`. I installed into ~/jbpm-3.3.0.GA
4. New > Other > Process Project
5. Go into src/main/jpdl/simple and open processdefinition.xml with jBPM Graphical Process Designer
6. Add a couple nodes, then connect them to the existing flow. Or create your own.
7. Switch to Source tab. I had this:

<?xml version="1.0" encoding="UTF-8"?>

<process-definition xmlns="urn:jbpm.org:jpdl-3.2" name="simple">

<start-state name="start-state1">
<transition to="state1"></transition>
</start-state>

<state name="state1">
<transition to="end-state2"></transition>
</state>

<end-state name="end-state2"></end-state>

</process-definition>

and gpd.xml contained this – three nodes in top-left to bottom-right cascade:

<?xml version="1.0" encoding="UTF-8"?>

<root-container name="simple" width="1058" height="740">
<node name="start-state1" x="32" y="19" width="132" height="36">
<edge>
<label x="5" y="-10"/>
</edge>
</node>
<node name="state1" x="77" y="103" width="132" height="36">
<edge>
<label x="5" y="-10"/>
</edge>
</node>
<node name="end-state2" x="115" y="203" width="132" height="36"/>
</root-container>

8. On the Source tab of the jBPM editor, select the middle state node and cut it out (CTRL-X). Note the outline view refreshes correctly.
9. Paste it back in, perhaps in the same location from where it was cut. (Use case: user wants to reorder the XML for personal taste reasons, or accidentally deleted and restored a block of XML).

10. Switch to diagram view. The middle node "state1" is now at (0,0) instead of where it used to be, eg., at (77,103)