The following forum message was posted by thanage at 
http://sourceforge.net/projects/pydev/forums/forum/293649/topic/3768079:

If you goto the Help menu and select Install new software, then click on the 
link What is already installed, then select the Configuration tab, then select 
the View Error Log button, I bet you will see what I am seeing, lots of file 
not found errors. The problem is the files are present in the specified 
locations. Do you want to submit a defect?

!MESSAGE Exception saving preferences to: 
C:/Users/thillestad/.eclipse/org.eclipse.platform_3.5.0_248562372/p2/org.eclipse.equinox.p2.engine/profileRegistry/epp.package.java.profile/.data/.settings/org.eclipse.equinox.p2.metadata.repository.prefs.
!STACK 0
java.io.FileNotFoundException: 
C:\\Users\\thillestad\\.eclipse\\org.eclipse.platform_3.5.0_248562372\\p2\\org.eclipse.equinox.p2.engine\\profileRegistry\\epp.package.java.profile\\.data\\.settings\\org.eclipse.equinox.p2.metadata.repository.prefs
 (The requested operation cannot be performed on a file with a user-mapped 
section open)
        at java.io.FileOutputStream.open(Native Method)
        at java.io.FileOutputStream.<init>(Unknown Source)
        at java.io.FileOutputStream.<init>(Unknown Source)
        at 
org.eclipse.core.internal.preferences.EclipsePreferences.save(EclipsePreferences.java:997)
        at 
org.eclipse.equinox.internal.p2.engine.ProfilePreferences.doSave(ProfilePreferences.java:137)
        at 
org.eclipse.equinox.internal.p2.engine.ProfilePreferences$SaveJob.run(ProfilePreferences.java:49)
        at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54)



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