I'm on Oneiric with all the -proposed updates, and I've been seeing this
issue for a month or longer, but I don't use any apps that do HTML5
notifications. The main time I seem to see these white boxes pop up is
when clicking links from another app (e.g. pidgin, hotot) that open in
chrome. Also the pages that cause it mostly seem to have Flash embeds.
Unfortunately it hasn't been 100% reproducible with any given link.

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https://bugs.launchpad.net/bugs/940603

Title:
  white box randomly shows up at top left corner blocking applications
  from using stuff under it

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