I found that I had this problem on a vanilla 8.04.1 install with the
'epiphany-browser' and 'ubuntu-restricted-extras' packages installed. I
could easily reproduce it on the Transmission in hardy-updates, as well
as intrepid, as well as a self-built (using pbuilder) 1.22 version by
downloading two (or more) torrents, removing one, then attempting to
download a new one.

One    -    Two   -   Three    -   [Three]
^             ^           ^              ^
Worked    Worked  Failed      Worked

Where [Three] is the same .torrent download, after removing the second
one.

My .xsession-errors file came up with:

GCJ PLUGIN: thread 0x816c470: NP_GetMIMEDescription
GCJ PLUGIN: thread 0x816c470: NP_GetMIMEDescription return
GCJ PLUGIN: thread 0x816c470: NP_GetValue
GCJ PLUGIN: thread 0x816c470: NP_GetValue: returning plugin name.
GCJ PLUGIN: thread 0x816c470: NP_GetValue return
GCJ PLUGIN: thread 0x816c470: NP_GetValue
GCJ PLUGIN: thread 0x816c470: NP_GetValue: returning plugin description.
GCJ PLUGIN: thread 0x816c470: NP_GetValue return

Each time I downloaded a .torrent that didn't appear in Transmission, I
use Epiphany as my main browser and the settings are the defaults,
including the "Automatically download and open files" being ticked.

Tristan's solution initially didn't work for me, my eventual fix was
two-fold:

I had to uninstall the openjdk packages (openjdk-6-jre) and install the
Sun Java packages instead (sun-java6-bin), then run 'update-java-
alternatives -s java-6-sun' to make the errors disappear, but it just
made the error appear after the 5th, or 6th torrent, rather than the
third.

I then changed the default MIME type to point to a custom application
called "/usr/bin/transmission", restarted my session and found it worked
with Firefox 3.x and Epiphany 2.22.x.

I then re-installed the openjdk-6-jre libraries (in order to test it
wasn't the MIME change alone that caused it) and Transmission started
bailing on the same conditions as it did originally.

Only question is, i've got no idea why downloading a .torrent would
spawn the GCJ plugin?

-- 
Transmission doesn't open torrents via Firefox 3
https://bugs.launchpad.net/bugs/204184
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