Possible temporary workaround:

I've had this problem quite a lot since upgrading while running matlab
as others have commented. Once the error message pops up, answering
yes/no/cancel all results in losing all window decorations.

However, if instead of answering the error message, if you merely
minimize the error dialog, the window decorations continue functioning
apparently indefinitely. I only have an N of one here, so YMMV, but
until the patches come, it appears to work for me.

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https://bugs.launchpad.net/bugs/727143

Title:
  unity-window-decorator crashes with SIGSEGV when closing Java windows

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