I am able to reproduce the problem as described by Andrew.
Even more so, any user typed settings are not preserved. However the True/False 
(showing an X) type of settings are preserved.
Another way to test is to cat the ~/aptitude/config file after any change. when 
the settings are preserved, the file is updated right way, no need to quit and 
reload.
Note that the user typed settings appear to be preserved as they are kept 
in-memory while the program is running but are lost when the program quits.
BugSquad

Linux ubuntu 2.6.24-23-generic #1 SMP Mon Jan 26 01:04:16 UTC 2009 x86_64 
GNU/Linux
Version: 0.4.9-2ubuntu5

** Changed in: aptitude (Ubuntu)
       Status: New => Confirmed

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aptitude does not retain settings
https://bugs.launchpad.net/bugs/252635
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