You can divert such JavaScript window.open() links to a new tab.
You can also open such links in the background.
You may have an extension that has changed such settings.

See http://kb.mozillazine.org/browser.link.open_newwindow.restriction

There are three prefs, accessible via the about:config page, to control the focus if you click a link.

browser.tabs.loadInBackground (normal links)
browser.tabs.loadDivertedInBackground (javascript)
browser.tabs.loadBookmarksInBackground (bookmarks and searchbar)

See also http://kb.mozillazine.org/about%3Aconfig_entries

I verified that browser.link.open_newwindow.restriction" is set to 2 and browser.tabs.loadDivertedInBackground (javascript) is set to false. From what I read from the info you provided, those would be the right settings.

So the problem remains but your efforts are appreciated nevertheless ...

Some programs install extension globally that Firefox install by default in a new profile.

Did you check that in the new profile (Tools > Add-ons > Extensions) ?

Yes I noticed some extensions that I did not install and I ass/u/me'd that they were not an issue. So I went back an checked on same and identified the culprits:

• Java QuickStarter -- added by the JRE
• Zone Toolbar -- add by the ZA security suite

Disabling these extensions took care of the problem. Thanks for your help ...

• • • Update ***

As it turns out, by solving this problem I also resolved another issue. After closing Firefox with multiple tabs open, the Firefox process remained active. I was unable to open Firefox until I terminated the active process. It didn't matter whether tabs were saved or not.

Disabling the Java QuickStarter and ZA Toolbar add-ons resolved this issue as well.