I am seeing the same problem. I have installed the debugging version of
pdftk as instructed and libgcj11-dbg, and still get the same stack
strace:

Error: Unexpected Exception in open_reader()
Unhandled Java Exception:
java.lang.NullPointerException
   at gnu.gcj.runtime.NameFinder.lookup(libgcj.so.11)
   at java.lang.Throwable.getStackTrace(libgcj.so.11)
   at java.lang.Throwable.stackTraceString(libgcj.so.11)
   at java.lang.Throwable.printStackTrace(libgcj.so.11)
   at java.lang.Throwable.printStackTrace(libgcj.so.11)

I can send you the original document and the offending, evince-edited
version.

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https://bugs.launchpad.net/bugs/774052

Title:
  Pdftk fails on PDF annotations added from Evince

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