Many settings, especially the most advanced ones, are not present in the User Interface (UI) options dialog.
Preference settings that are modified from default values are saved in the prefs.js file. Instead of directly editing this file, recent Mozilla applications include a configuration editor that can be accessed from the application interface.
Source: Editing configuration
In Firefox, type about:config in the Location Bar (address bar) and press Enter to display the list of preferences [...]. If you see a page with the warning message, "This might void your warranty!", click the button labeled "I'll be careful, I promise!", to continue (in fact, there is no warranty whatsoever, it's more a joke to ensure that users are aware of what they are about to do). Use the checkbox there to avoid the warning in the future.
To add a new preference, context-click (right-click) anywhere in the list of preferences. In the context menu, select New then select the type of preference you are adding.
To modify an existing preference, context-click (right-click) on the preference, select Modify and type in the new value.
To reset a preference to its default value or to remove an added preference, context-click (right-click) on the preference and select Reset.
You can use the Search bar at the top of the about:config page to filter the preferences that you want to inspect. The search bar is case-insensitive, unlike the actual configuration variables.
Source: about:config
browser.link.open_newwindow
Type Integer
Default value 3
Description Controls where to open links that would normally open in a new window. Possible values:
1 (or anything else) - open in the current tab or window.2 - open in a new window.3 - open in a new tab.
Enabling or disabling the Open new windows in a new tab instead UI option will toggle this preference between 3 and 2.
browser.link.open_newwindow.restriction
Type Integer
Default value 2
Description Restricts all new windows opened by JavaScript. Possible values:
0 - always force new windows into tabs.1 - don't restrict new windows.2 - force windows that don't specify their features (e.g. width, height) into tabs.
browser.popups.showPopupBlocker
Type Boolean
Default value true
Description Determines whether to show an icon in the status bar when a pop-up has been blocked. Obsolete, just leave it as-is.
dom.disable_open_click_delay
Type Integer
Default value 1000
Description Handles pop-ups according to the current pop-up blocker settings when created through a JavaScript timing event using a delay smaller than this value (in milliseconds).
dom.disable_open_during_load
Type Boolean
Default value true
Description When enabled, blocks pop-ups created while the page is loading. This setting is equivalent to the Block pop-up windows UI option.
dom.disable_window_flip
Type Boolean
Default value true
Description Determines whether windows can be focused through JavaScript.
dom.disable_window_move_resize
Type Boolean
Default value false
Description Determines whether windows can be moved or resized using JavaScript.
dom.disable_window_open_feature.*
Description Rather than a single preference, this is a set of different boolean settings which can prevent a specific pop-up feature (e.g. address bar, scroll bars, etc.) from being disabled when set to true. Available preferences:
dom.disable_window_open_feature.closedom.disable_window_open_feature.locationdom.disable_window_open_feature.menubardom.disable_window_open_feature.minimizabledom.disable_window_open_feature.personalbardom.disable_window_open_feature.resizabledom.disable_window_open_feature.scrollbarsdom.disable_window_open_feature.statusdom.disable_window_open_feature.titlebardom.disable_window_open_feature.toolbar
dom.disable_window_status_change
Type Boolean
Default value true
Description When enabled, prevents the status bar text from being changed via JavaScript.
dom.popup_allowed_events
Type String
Default value change click dblclick mouseup reset submit touchend
Description A space-separated list of the events allowed to create pop-ups. Although undocumented, setting the value to a single space character will create an empty list, thus disabling all pop-ups (exceptions still apply). The same effect can be achieved by specifying a non-existent event (e.g. none).
dom.popup_maximum
Type Integer
Default value 20
Description Limits the number of simultaneously open pop-up windows.
privacy.popups.disable_from_plugins
Type Integer
Default value 2
Description Controls pop-ups created by plug-ins (e.g. Adobe Flash Player). Possible values:
0 - no restrictions.1 - limits the pop-ups number to dom.popup_maximum.2 - block all pop-ups except for whitelisted websites.3 - block all pop-ups.
privacy.popups.policy
Type Integer
Default value 1
Description Deprecated. Use dom.disable_open_during_load instead.
privacy.popups.showBrowserMessage
Type Boolean
Default value true
Description Determines whether to display an information bar whenever one ore more pop-us are blocked. Can be changed by using the Don't show info bar when pop-ups are blocked UI option.
privacy.popups.usecustom
Type Boolean
Default value true
Description Apparently unused.
These are the values I currently use for the settings listed above; feel free to experiment with other settings on your own. Tested with Firefox 27.0.1.
Best Answer
Affecting both Microsoft Internet Explorer and Firefox seems highly unlikely to happen by accident, because they are completely separate implementations. (For fun, you could also try Google Chrome.)
The most likely reason I can think of is some sort of "anti-virus" protection software affecting the behaviors of these browsers.
(The next-most-likely reason I can think of is someone disabling JavaScript support, manually, in both browsers.)