I just recognized that synaptic has finished applying the new option -- after 
about 30 minutes of no response (I did not kill the process because I wanted to 
see if anything happens eventually). During that time synaptic occupied my CPU 
by around 90%. Thus, Synaptic does not crash as mentioned in the title but 
instead only has some difficulties in changing this option in acceptable time.
The changed setting still is in effect after having started a new session.
When I now re-enable this option and click ok, synaptic does again not respond 
due to high CPU load. In 'top' I first observed about 50% synaptic and 40% 
at-spi-registry (whatever that is) for about 10 seconds. Then, synaptic raised 
to 90-95% and at-spi-registry decreased to 2% (don't know if this helps), which 
is still the case (~10 minutes later)...

-- 
synaptic crashes in Lucid when deselecting "Consider recommended packages as 
dependencies"
https://bugs.launchpad.net/bugs/661860
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