After further investigation it seems that the contents of the
.azureus/logs/save directory are what is used to determine whether it
shut down properly. There is some kind of timestamp/unique id in the
filenames, and it looks at the one for the previous launch when it
starts. This is why removing the directory works. I couldn't reproduce
because a "killall" of the Sun JVM doesn't seem to give azureus time to
write into this directory (should this be another bug?). The following
describes the possibilities:

1) Start Azureus under GCJ.
2) Issue "killall java" (don't be running other java programs). This should 
allow Azureus to write logs into logs/save to look for at next startup.
3) Start Azureus under GCJ, note that it works, gives error message about 
previous shutdown, shutdown properly.
4) Start Azureus under either JVM, note that acknowledging the message/correct 
shutdown has fixed the problem (presumably updated timestamp/unique id to look 
for in logs/save).
5) Repeat steps 1 and 2.
6) Remove .azureus/logs/save
7) Start Azureus under either JVM, note that it works.
8) Repeat steps 3 and 4.
9) Start under Sun JVM, note that it fails.

So either reading the previous shutdown error in .azureus/logs/save or
displaying the message about it fails under Sun JVM (1.5). GIven that
these informational messages have had problems in the past and the
hotspot error seems to talk about moving/resizing GUI stuff, I think it
has to be the display of the dialog. Can other people confirm this?

-- 
Azureus 2.5.0.0 crashes
https://launchpad.net/bugs/68020

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