Tried to get transmission to call a script on download completion but it wasn't working. Checked /var/log/syslog and saw that the script was blocked by apparmor, specifically the /usr/lib/firefox/firefox{,*[^s][^h]}//sanitized_helper profile.
Running sudo apparmor_status will also show which profiles have been triggered and by which processes.
Turns out the problem exists when transmission is launched by clicking a link in firefox. If I start transmission from the command line, the script runs successfully!
Using transmission 2.51 (13280) and Ubuntu Precise 12.04.1 LTS
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