Grey structure in Jmol display and not linked to alignment display in jalview lite structure example

The FER1_MAIZE and 1gaq.txt example available from the applets examples page does not work properly. Whilst the associated structure is opened, the structure is grey (indicating it is not linked to the alignment window), and the 'View Mapping' menu entry doesn't work.

The console is also full of exceptions (produced from http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/applet/debug/applets.html):

applet context: -applet
appletDocumentBase=http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/applet/debug/applets.html
appletCodeBase=http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/applet/debug/
(C) 2009 Jmol Development
Jmol Version: 12.2.4 2011-10-11 21:29
java.vendor: Apple Inc.
java.version: 1.6.0_33
os.name: Mac OS X
memory: 25.0/85.0
processors available: 4
useCommandThread: false
appletId:panel10_jmol_jalview.appletgui.AppletJmolBinding@68de59f0

FileManager.getAtomSetCollectionFromFile(http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/applet/debug/1gaq.txt)
FileManager opening http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/applet/debug/1gaq.txt
The Resolver thinks Pdb
openFile(http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/applet/debug/1gaq.txt): 131 ms
reading 690 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
690 atoms created
Time to autoBond: 4 ms
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol 12.2.4 2011-10-11 21:29 DSSP analysis for model 1.1 - 1GAQ

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,
and we thank the CMBI for maintaining it to the extent that it was easy to
re-engineer for our purposes. At this point in time, we make no guarantee
that this code gives precisely the same analysis as the code available via license
from CMBI at http://swift.cmbi.ru.nl/gv/dssp

All bioshapes have been deleted and must be regenerated.

Squashed Jmol callback handler error:
java.security.AccessControlException: access denied (java.util.PropertyPermission user.dir read)
at java.security.AccessControlContext.checkPermission(AccessControlContext.java:374)
at java.security.AccessController.checkPermission(AccessController.java:546)
at java.lang.SecurityManager.checkPermission(SecurityManager.java:532)
at java.lang.SecurityManager.checkPropertyAccess(SecurityManager.java:1285)
at java.lang.System.getProperty(System.java:667)
at java.io.UnixFileSystem.resolve(UnixFileSystem.java:118)
at java.io.File.getAbsolutePath(File.java:501)
at jalview.ext.jmol.JalviewJmolBinding.getPdbFile(JalviewJmolBinding.java:696)
at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1075)
at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:975)
at org.jmol.viewer.StatusManager.setFileLoadStatus(Unknown Source)
at org.jmol.viewer.Viewer.setFileLoadStatus(Unknown Source)
at org.jmol.viewer.Viewer.createModelSetAndReturnError(Unknown Source)
at org.jmol.viewer.Viewer.loadModelFromFile(Unknown Source)
at org.jmol.viewer.Viewer.openFile(Unknown Source)
at jalview.appletgui.AppletJmol.<init>(AppletJmol.java:264)
at jalview.appletgui.AlignFrame.newStructureView(AlignFrame.java:3573)
at jalview.bin.JalviewLite$LoadingThread.startLoading(JalviewLite.java:2094)
at jalview.bin.JalviewLite$LoadingThread.run(JalviewLite.java:1771)

The offending line is:
JalvewJmolBinding.java:696: mset[0] = new File(m).getAbsolutePath();