Hi,
thanks for the report. Is there a crash log of unity-2d-panel in your 
/var/crash directory by any chance?

The error message:
Window manager warning: Window 0x46003e6 (win1) sets an MWM hint indicating it 
isn't resizable, but sets min size 1 x 1 and max size 2147483647 x 2147483647; 
this doesn't make much sense.
is new to me, and possibly a symptom/cause.

Also, this might sound unusual, but have you tried clicking in the area that 
the panel was in? We have a bug report where the panel just becomes invisible, 
bug 894493. Just on the off-chance this is what's occurring.
Thanking you
-G

** Also affects: unity-2d
   Importance: Undecided
       Status: New

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https://bugs.launchpad.net/bugs/944007

Title:
  unity-2d-panel crashes occasionally after launching NetBeans

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