I've looked at the code again and I finally found what causes this bug!

>From Raring to Saucy, there were these changes to the file
softwarecenter/config.py:

33c33
< class SoftwareCenterConfig(object, SafeConfigParser):
---
> class SoftwareCenterConfig(SafeConfigParser):
38d37
<         object.__init__(self)

The Software Center is executed using Python 2 (still?), so this changes the 
class from a "new style class" to an "old style class", I think. It seems 
Python properties don't work correctly in "old style classes".
Reverting these changes fixes the issue.

I've attached a patch that fixes the issue by reverting the changes.
I've tested this by editing the installed code directly and running 
software-center. The settings are now saved correctly and I haven't noticed any 
other new issues.
(By the way, I don't know if the line "object.__init__(self)" is really needed.)

---

However, I researched a bit to find why this change was made and, apparently, 
it was to fix a bug.
The changes were introduced in revision 3308 of lp:software-center by Rodney 
Dawes to fix bug LP:1038429 .
Software Center hasn't crashed for me, but I have apport disabled (the large 
number of crash reports in the first weeks of Saucy were too annoying).

So, someone with more knowledge about the code should look into this.

** Patch added: "fix_settings_not_saved.patch"
   
https://bugs.launchpad.net/ubuntu/+source/software-center/+bug/1244493/+attachment/4009827/+files/fix_settings_not_saved.patch

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https://bugs.launchpad.net/bugs/1244493

Title:
  Software Center doesn't save settings on Saucy

Status in Ubuntu Software Center:
  New
Status in “software-center” package in Ubuntu:
  Confirmed

Bug description:
  Certain settings will be reset for some odd reason whenever I quit the 
Software Center. Here's the main two areas where I notice this issue, both 
accessible under "View" in the global menu:
  1) Attempting to toggle on or off the option "New Applications in Launcher", 
regardless of what it's set to upon an exit and repopening of the Software 
Center it's set back to the default option of a check, meaning it will show new 
applications in the launcher regardless of what the user has set it to.
  2) Attempting to select the option "Turn on Recommendations..."  will also 
alow me to turn them on, but upon closing and opening up the Software Center 
again, I have to re-enable recommendations if I want them

  Running Ubuntu 13.10 Suacy with all the latest updates, with the
  latest version of the Software Center (13.10). Yes I have proposed
  updates enabled, but this may have happened at first with the original
  package in Saucy as well. Regardless, these are official packages and
  this is a usability bug in need of a fix. The settings don't save (I
  remember they saved in previous Ubuntu versions) but they no longer
  do. Obviously, these settings should save somewhere for a consistent
  experience.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.10
  Package: software-center 13.10-0ubuntu1
  ProcVersionSignature: Ubuntu 3.11.0-12.19-generic 3.11.3
  Uname: Linux 3.11.0-12-generic x86_64
  ApportVersion: 2.12.5-0ubuntu2.1
  Architecture: amd64
  Date: Thu Oct 24 21:59:17 2013
  InstallationDate: Installed on 2013-10-17 (7 days ago)
  InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Release amd64 
(20131016.1)
  MarkForUpload: True
  PackageArchitecture: all
  SourcePackage: software-center
  UpgradeStatus: No upgrade log present (probably fresh install)

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