I thought it was something from testing but on 8/24 I I downloaded 12.04.1 and reinstalled - yes I used my updated 5 year old template to make Ubuntu as I want:

Code:
Add First: Synaptic, Gconf-editor, Gnome-panel, Indicator-applet-session
  Desktop Theme: Radiance
Add (as desired): Audacity, Avidemux, Bleachbit, Boinc, Checksecurity, Chkrootkit, Conky*, Create-resources, Ffmpeg, Flac, Gdebi(??), GoogleEarth, Hddtemp, Hplip-gui, K3b*, Kompozer, LibosMesa6, LibreCad, LibreOfficePDFImport, LMsensors, Localepurge, Lsb-core, Mesa-utils, Mozilla-Plugin-Vlc, Mozplugger, Mplayer, Samba, Sane, Sensord, Smbfs, System-config-samba, Ubuntu_restricted*,Vlc, Wine 1.4, Xsane | * Multiple files, as required
Edit Gnome Functions: gconf-editor: apps > gnome-terminal > keybindings - Change copy/paste: CTRL | > metacity > general > button_layout - Change to ":minimize,maximize,close" | desktop > gnome > interface > toolbar_style - Change to "text" | thumbnailers - disable_all
 System Tools > System Settings > Keyboard > Shortcuts > System > Show the run command prompt.
 System Tools > System Settings > Brightness & Lock>Lock=Off.
 sudo gsettings set com.ubuntu.update-notifier auto-launch false
 sudo gsettings set org.gnome.desktop.interface menus-have-icons false
 sudo gsettings set org.gnome.desktop.interface buttons-have-icons false
Show all Start Up Options: sudo sed -i 's/NoDisplay=true/NoDisplay=false/g' /etc/xdg/autostart/*.desktop
Disable Guest account: gksudo gedit /etc/lightdm/lightdm.conf | Add at end of the file: allow-guest=false
Add to Top Panel: Gedit, Take Screenshot, Terminal 
Add Hardware Graphics - ATI: After installing ATI Driver: sudo aticonfig --initial -f
Firefox AddOns: AskForSanitize, BetterPrivacy, Video DownloadHelper, FireFTP, Littlefox, NoScript, RefControl, ReloadEvery, take me to this URL, User Agent Switcher, Zoom Page.
Firefox Tab view Cancel: browser.newtab.url-change from about:newtab to about:blank | browser.newtabpage.enabled-change to FALSE.
Firefox Search Engine Addition: (https://encrypted.google.com/): Copy file egoogle.xml to new folder"searchplugins
Firefox userChrome.css to move "Open Link in New Window" to the top of the context menu:  @namespace url("http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"); /* only needed once */ #contentAreaContextMenu > * { -moz-box-ordinal-group: 2; } #context-openlink { -moz-box-ordinal-group: 1 !important; } 
Set up OpenDNS: IPv4 Settings: to Automatic (DHCP) addresses only. Add DNS Servers: 208.67.222.222, 208.67.220.220
Add Programs:   BitDefender (help.ubuntu.com/community/BitDefender) - | Medibuntu (help.ubuntu.com/community/Medibuntu)  
Remove (if installed): Aislerot, Bluez*, Colord, DejaDup, Empathy*, Evolution*, Example-content, Gnome-games*, Gnome-online-accounts, Gnome-orca, Gwibber*, Ibus-pinyin, Indicator-messages, Mobile-broadband-providers, Modemmanager, Oneconf, (OK to remove Ubuntu-desktop), Remmina*, Rhythmbox*, Ryslog, Shotwell, Telepathy*, Telnet, Toshet, Totem*, Unneeded Fonts*, Ubuntu-one, Unity-scope-video-remote, Vino, Whoopsie, Zeitgeist |* Multiple files, as required
Conky: conkyrc., edit as needed. Autostart path is: /home/your user name/.conky_start.sh 
Sensors: After installing lm_sensors run sudo sensors-detect. Also sudo dpkg-reconfigure hddtemp  
Firefox Tweaks:  breakpad.reportURL=remove | browser.bookmarks.max_backups=2 | browser.chrome.site_icons=f | browser.chrome.favicons=f | browser.sessionhistory.max_entries=5 | browser.sessionstore.max_tabs_undo=3 | browser.sessionstore.max_windows_undo=1 | dom.popup_maximum=5 | dom.storage.enabled = false | geo.enabled=false | layout.spellcheckDefault=2 | network.http.max-connections-per-server=30 | network.http.max-persistent-connections-per-proxy=12 | network.http.max-persistent-connections-per-server=12 | network-prefetch-next=false | plugin.expose_full_path=T | services.sync=set most boolean to false | network-websocket* =  false | browser.urlbar.autoFill = false*  
Also Enable “When an OCSP server connection fails, treat the certificate as invalid” | enable SSL 3.0, TLS 1.0.
Thunderbird Tweaks:  Edit > Preferences > Advanced > General > | Global Search... - Uncheck |Config Editor: Toggle - mail.tabs.autoHide | Install:  extra_folder_columns-1.1.3-tb.xpi, profilepass-TB-RDF-0.7.17.xpi
Add/Confirm Optional Other PPA (confirm first-may need key):  deb-src http://extras.ubuntu.com/ubuntu precise main | deb http://download.bitdefender.com/repos/deb/ bitdefender non-free | deb-src http://download.bitdefender.com/repos/deb/ bitdefender non-free | deb http://archive.getdeb.net/ubuntu precise-getdeb games apps | deb-src http://archive.getdeb.net/ubuntu precise-getdeb games apps | deb http://ppa.launchpad.net/libreoffice/ppa/ubuntu precise main | deb-src http://ppa.launchpad.net/libreoffice/ppa/ubuntu precise main   
Firefox 7+ - userchrome.css:  Go to /home/YOUR_USERNAME/.mozilla/firefox/yourprofile.default/chrome - if the "chrome" folder doesn't exists, create it and create "userChrome.css" inside this folder.
OK, so why, AGAIN do I not have the ability to run Synaptic from the dropdown Menu, I can NOT change settings in Software Sources (can change but are not saved) and does it STILL seem to be checking and even downloading unauthorized updates to the program without my approval?

This did seem to work originally, but I have not booted into 12.04.1 in 3 days and somehow it is back to doing what it was with 12.04.00 (see other recent posts..)

Anyone have an answer?

Thank you.