If there are other windows open and you use the close X on the title bar then you only close that specific window, but you do not close the current session.
You can use History > Recently Closed Windows to restore that window and try again.
You need to use Firefox/File > Exit to close all open windows at once and exit Firefox to restore the current session. Or you have to close other open browser windows first if you do not want to restore them.

Thanks but as I said when only popup window is open you CAN'T access the menu to undo the damage. The popup windows should not be threated as separate windows, but it should be part of the parent windows( so if I close the parent window, it should too ). I know that I should close unwanted windows first but if there is some small window on the background, you don't see it... So it would be cool to be able to configure the behaviour of X.

You can set the warn prefs on the about:config page to true via the right-click context menu or toggle the value with a double left-click.

• browser.showQuitWarning, see http://blog.zpao.com/post/3174360617/about-that-quit-dialog
• browser.tabs.warnOnClose, see http://kb.mozillazine.org/About%3Aconfig_entries
• browser.warnOnQuit , see http://kb.mozillazine.org/browser.warnOnQuit
• browser.warnOnRestart , see http://kb.mozillazine.org/browser.warnOnRestart

To open the about:config page, type about:config in the location (address) bar and press the "Enter" key, just like you type the url of a website to open a website.
If you see a warning then you can confirm that you want to access that page.
You can use the Filter bar at to top of the about:config page to locate a pref more easily.

Thanks, I can set up the warning. And what about that popup window idea (that it should close with parent)?

It is always a good idea to close a Firefox session by clicking File > Exit or Firefox button > Exit for proper shutdown.

Those pop-up windows are produced by JavaScript. JavaScript can disable certain features in the pop-up window. You can set some preferences using about:config so that those features are not disabled in the pop-up window. See:

• How to use about:config: http://kb.mozillazine.org/About:config

1. type about:config in the URL/Location bar and press the Enter key
2. if you see a warning, accept it (promise to be careful)
3. Filter = dom. disable_window_open_feature.
4. reset preferences you want to false by double-clicking on that preference in the lower panel on the about:config tab
5. Preferences you can reset in this case: http://kb.mozillazine.org/Prevent_websites_from_disabling_new_window_features

You need to update the following. The Plugin version(s) shown below was/were submitted with your question and is/are out of date. You should update to avoid known security issues with the version(s) you have installed. Click on "More system info..." to the right of your question to see what was included with your question.

• Adobe PDF Plug-In For Firefox and Netscape "9.4.3"
• Shockwave Flash 10.2 r159
• Next Generation Java Plug-in 1.6.0_24 for Mozilla browsers

1. Check your plugin versions on either of the following links':
   • http://www.mozilla.com/en-US/plugincheck/
   • https://www-trunk.stage.mozilla.com/en-US/plugincheck/
   • Note: plugin check page does not have information on all plugin versions
   • There are plugin specific testing links available from this page:
     • http://kb.mozillazine.org/Testing_plugins
2. Update Adobe Reader (PDF plugin):
   • From within your existing Adobe Reader (if you have it already installed):
     • Open the Adobe Reader program from your Programs list
     • Click Help > Check for Updates
     • Follow the prompts for updating
     • If this method works for you, skip the "Download complete installer" section below and proceed to "After the installation" below
   • Download complete installer (if you do NOT have Adobe Reader installed):
     • SAVE the installer to your hard drive (save to your Desktop so that you can find it after the download). Exit/Close Firefox. Run the installer you just downloaded.
     • Use either of the links below:
       • https://support.mozilla.com/en-US/kb/Using+the+Adobe+Reader+plugin+with+Firefox (click on "Installing and updating Adobe Reader")
       • Also see Download link': http://get.adobe.com/reader/otherversions/
   • After the installation, start Firefox and check your version again.
3. Update the Flash plugin to the latest version.
   • Download and SAVE to your Desktop so you can find the installer later
   • If you do not have the current version, click on the "Player Download Center" link on the "Download and information" or "Download Manual installers" below
   • After download is complete, exit Firefox
   • Click on the installer you just downloaded and install
     • Windows 7 and Vista: may need to right-click the installer and choose "Run as Administrator"
   • Start Firefox and check your version again or test the installation by going back to the download link below
   • Download and information: http://www.adobe.com/software/flash/about/
     • Use Firefox to go to the above site to update the Firefox plugin (will also install plugin for most other browsers; except IE)
     • Use IE to go to the above site to update the IE ActiveX
   • Download Manual installers.
     • http://kb2.adobe.com/cps/191/tn_19166.html#main_ManualInstaller
     • Note separate links for:
       • Plugin for Firefox and most other browsers
       • ActiveX for IE
4. Update the Java plugin to the latest version.
   • Download site: http://www.oracle.com/technetwork/java/javase/downloads/index.html (Java Platform: Download JRE)
     • Be sure to un-check the Yahoo Toolbar option during the install if you do not want it installed.
   • Also see "Manual Update" in this article to update from the Java Control Panel in Windows Control Panel: http://support.mozilla.com/en-US/kb/Using+the+Java+plugin+with+Firefox#Updates
   • Removing old versions (if needed): http://www.java.com/en/download/faq/remove_olderversions.xml
   • Remove multiple Java Console extensions (if needed): http://kb.mozillazine.org/Firefox_:_FAQs_:_Install_Java#Multiple_Java_Console_extensions
   • Java Test: http://www.java.com/en/download/help/testvm.xml