What's with all of the squares of text that pop up?

I just bought my first mac in over 4 years. What is with all of the pop ups? I disabled the tool tips in Firefox, but I still get white boxes that pop up at the oddest times. What can I do to disable them? Some of them seem to be connected to Flash Player.
Thanks in advance for any help you can give me. They're driving me crazy! I'm running Lion.

Can you tell if these are generated by the browser (i.e. ads or browser-specific tooltips), or are they generated by the operating system or component, such as Java?
I unfortunately don't have an answer for you, but I am using Safari, and I get random Java po-up windows causing anything full-screen to jump back to normal view, etc.  If you're having the same issues as I am, then I'd be happy to get an answer as well.  I've updated to the latest OS release from Apple, updated my Java, flash, etc.  I'm still getting pop-up windows.  The windows, however, close by themselves.  They pop up for only a second or so, and then close.
Same issue?

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