Firefox 31 (Ubuntu) won't open new window or Javascript pop-ups

Hi, I am running Firefox 31.0 in Ubuntu 14.04 having the following problem:
1) When I click on New Window or New Private Window in the File menu, nothing happens, same with pressing Ctrl-N.
2) Certain websites are not able to open new windows or pop-up windows through Java or Javascript
(e.g. the command: javascript:popup_imp(...) does not produce anything)
I did try safe-mode and there everything works fine. Then I restarted firefox (several times) with all plugins disabled but still had the same problem, so I don't know what causes the difference between safe-mode and no plugins.
(By the way, there is no problem opening a New Tab by pressing Ctrl-T or from the file menu, the issue is only the New Window and New Private Window).
Is there any other way to narrow down what is preventing the new windows?

Hi cor-el,
thanks for your answer, however as I explained in my post, safe-mode does not present the problem, but disabling the extensions on its own does not help (i.e with all extensions disabled the problem still is there).
Also, I did not have this problem in the past and I did not change anything graphics related (unless something was changed software-wise internally and I did not notice).
And yes I am currently using the default theme.

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