I can confirm this is still happening. For me only the default search engines 
are affected, meaning google.com, duckduckgo.com, ebay.com, amazon.com, 
twitter.com, wikipedia (english) and yahoo.com.
The must get readded as they also are listed on bottom in the list of search 
engines after every update AND more importantly are readded although I usually 
delete most of them anyway.

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https://bugs.launchpad.net/bugs/936920

Title:
  [regression] default search engines are readded (keywords wiped) with
  upgrade

Status in “firefox” package in Ubuntu:
  Confirmed
Status in “iceweasel” package in Debian:
  Fix Released

Bug description:
  Original Bug:
  https://bugs.launchpad.net/firefox/+bug/428306

  
  i had detected, that the original search engines are added with an update!

  ProblemType: Bug
  DistroRelease: Ubuntu 11.04
  Package: firefox 10.0.2+build1-0ubuntu0.11.04.1
  ProcVersionSignature: Ubuntu 2.6.38-13.55-generic 2.6.38.8
  Uname: Linux 2.6.38-13-generic x86_64
  NonfreeKernelModules: fglrx
  AddonCompatCheckDisabled: False
  AlsaVersion: Advanced Linux Sound Architecture Driver Version 1.0.23.
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  frank      2290 F.... xfce4-volumed
   /dev/snd/controlC0:  frank      2290 F.... xfce4-volumed
                        frank      2302 F.... pulseaudio
  BuildID: 20120216100510
  CRDA: Error: [Errno 2] Datei oder Verzeichnis nicht gefunden
  Card0.Amixer.info:
   Card hw:0 'SB'/'HDA ATI SB at 0xfe024000 irq 16'
     Mixer name : 'Realtek ALC889A'
     Components : 'HDA:10ec0885,1458a102,00100101'
     Controls      : 38
     Simple ctrls  : 21
  Card1.Amixer.info:
   Card hw:1 'HDMI'/'HDA ATI HDMI at 0xfdffc000 irq 19'
     Mixer name : 'ATI RS690/780 HDMI'
     Components : 'HDA:1002791a,00791a00,00100000'
     Controls      : 4
     Simple ctrls  : 1
  Card1.Amixer.values:
   Simple mixer control 'IEC958',0
     Capabilities: pswitch pswitch-joined penum
     Playback channels: Mono
     Mono: Playback [on]
  Channel: release
  Date: Mon Feb 20 13:10:15 2012
  ForcedLayersAccel: False
  IncompatibleExtensions:
   Leo Search - ID={c666c018-6409-4479-afa3-68e4129e7eff}, Version=1.1.0, 
minVersion=3.5, maxVersion=8.*, Location=app-profile, Type=extension, Active=Yes
   NoScript - ID={73a6fe31-595d-460b-a920-fcc0f8843232}, Version=2.3, 
minVersion=1.9a2, maxVersion=1.9.6, Location=app-profile, Type=extension, 
Active=Yes
  InstallationMedia: Xubuntu 10.04.2 "Lucid Lynx" - Release amd64 (20110215.1)
  IpRoute:
   192.168.0.0/24 dev eth0  proto kernel  scope link  src 192.168.0.101  metric 
1 
   169.254.0.0/16 dev eth0  scope link  metric 1000 
   default via 192.168.0.1 dev eth0  proto static
  IwConfig:
   lo        no wireless extensions.
   
   eth0      no wireless extensions.
   
   vboxnet0  no wireless extensions.
  ProcEnviron:
   LANGUAGE=de_DE:en
   LANG=de_DE.UTF-8
   SHELL=/bin/bash
  Profiles: Profile0 (Default) - LastVersion=10.0.2/20120216100510 (Running)
  RfKill:
   
  RunningIncompatibleAddons: True
  SourcePackage: firefox
  UpgradeStatus: Upgraded to natty on 2012-01-02 (48 days ago)
  dmi.bios.date: 07/08/2010
  dmi.bios.vendor: Award Software International, Inc.
  dmi.bios.version: F7c
  dmi.board.name: GA-MA790GP-UD4H
  dmi.board.vendor: Gigabyte Technology Co., Ltd.
  dmi.board.version: x.x
  dmi.chassis.type: 3
  dmi.chassis.vendor: Gigabyte Technology Co., Ltd.
  dmi.modalias: 
dmi:bvnAwardSoftwareInternational,Inc.:bvrF7c:bd07/08/2010:svnGigabyteTechnologyCo.,Ltd.:pnGA-MA790GP-UD4H:pvr:rvnGigabyteTechnologyCo.,Ltd.:rnGA-MA790GP-UD4H:rvrx.x:cvnGigabyteTechnologyCo.,Ltd.:ct3:cvr:
  dmi.product.name: GA-MA790GP-UD4H
  dmi.sys.vendor: Gigabyte Technology Co., Ltd.

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