Hi there,
I have the same problem. Here is what I did
1) Install Eclipse 3.2 standoline (not using apt-get)
2) Manually install all plugins (download and extract)
3) you MUST change the default JVM to the Sun JVM - I spent 4 hours on this, 
but Eclipse PDT does NOT work with the default Ubuntu JVM, you must switch to 
the Sun JVM.

sudo update-alternatives --config java

and select the sun jvm

Hope this helps

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Eclispe installs but does not upgrade nor allows installing of PDT!!
https://bugs.launchpad.net/bugs/82422
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