Firefox opens new windows under the current window

Whenever I right-click on a link and tell it to open in a new window, the window opens behind the current window. I have selected "When I open a link in a new tab, switch to it immediately". That used to solve this problem but seems to have stopped working.
I have read all the threads on this problem, including the one saying it's caused by Flash.
However, I have checked in safe mode and I still get the same problem.
This started happening around Christmas on three computers. Since then, because of problems getting a driver to install for a new peripheral, I have done a fresh install of Windows 7 64 bit, reinstalled FF newest version and restored my profile, but get the same problem. At this point I have started in the FF safe mode which should disable all the add-ons, but the same thing still happens. I have also reset FF using the reset option in the help menu. It doesn't always happen, but it can happen when flash is already running in another window.
Are there a series of steps I can take which will verify that the fault is caused by Flash? I had thought the safe mode would do that.
Honestly, this is enough of a problem to make me switch browsers, and I don't even like any of the other browsers. If you can offer any other suggestions I would really appreciate it.

Safe Mode actually doesn't disable Flash. It's a little confusing: it disables extensions, but not plugins, so "Restart with Add-ons Disabled" is really not a very good description.
If you want to test with Flash disabled, you can set it to "Never Activate" temporarily. Open the Add-ons page using either:
* Ctrl+Shift+a
* orange Firefox button (or Tools menu) > Add-ons
In the left column that lists the categories, click Plugins. You're looking for "Shockwave Flash." Change it to "Never Activate."
You can keep this tab open during your testing. If you close and re-open the Add-ons page, Shockwave Flash will fall to the bottom with the other disabled plugins.

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