I had this problem, or at least a similar problem, too.

I left Transmission running over the weekend to seed. When I tried
quitting it this morning, it said to hold on while it was uploading
stats to the tracker. After a couple of hours I noticed it hadn't
finished, so I closed the window. After a bit I got the dialog saying it
wasn't going quietly; I told it to go ahead and kill the app.

That still didn't do anything, and ps still showed it consuming 100% of
the CPU. I repeatedly tried killing it, both normally and -9. The
process still appeared to be running, and my load was high (over 5).
Looking further I saw that the CPU-eating process had a parent, so I
tried to kill -9 both of those. It didn't work, but shortly after that
the machine locked up and I had to reboot.

I thought it might be just my machine, but Google suggests a number of
people report similar symptoms, so it seems like there's some unhappy
interaction between Transmission and the kernel.

I'm using a reasonably fresh Ubuntu box that is otherwise unproblematic.
Software versions:

Ubuntu 10.04.1 LTS
Linux bluegum 2.6.32-25-generic #45-Ubuntu SMP Sat Oct 16 19:52:42 UTC 2010 
x86_64 GNU/Linux
transmission-common 1.93-0ubuntu0.10.04.1
transmission-gtk 1.93-0ubuntu0.10.04.1

-- 
Transmission does not respond/Icon remains in notification area after closing 
program
https://bugs.launchpad.net/bugs/530176
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