Strange menu bars appearing

Hello!
Today when I was doing my physics simulations a strange thing appeared.
A menu bar like in the app not in fullscreen mode appeared. With no content. Just empty menu bar and it appered in front of fullscreen mode Xcode/Safari/Mail. And the worst thing was that I wasn't able to kill it. When I clicked on that, nothing happened. Then after a some time (I wasn't near my Mac all the time, but I was in room where it is) there showed up another dummy bar. When I restarted my Mac, it doesn't repeated at all.
May it be the malware?
But I'm not running pirated software, all software I have - is opensource/buyed/downloaded from the developer (AppCleaner, Amazon Kindle).
I started ClamXav scan, but it didn't find anything at all.
What may be that?
P.S. I forget to take screenshots, sorry for that.
P.P.S. I was running SSH connection to the server about 17 hours long.

I found those logs to be "non-standard"(i.e. not com.apple.WebKit, WindowServer, kernel e.t.c.):
26/04/14 18:57:51,620 Preview[7742]: It does not make sense to draw an image when [NSGraphicsContext currentContext] is nil.  This is a programming error. Break on void _NSWarnForDrawingImageWithNoCurrentContext() to debug.  This will be logged only once.  This may break in the future.
26/04/14 19:29:11,109 UserNotificationCenter[7044]: Unable to simultaneously satisfy constraints:
    "<NSLayoutConstraint:0x7fc721487240 H:[_NSAlertContentView:0x7fc721539d80(>=420)]>",
    "<NSLayoutConstraint:0x7fc721487290 H:[_NSAlertContentView:0x7fc721539d80(<=1)]>"
Will attempt to recover by breaking constraint
<NSLayoutConstraint:0x7fc721487290 H:[_NSAlertContentView:0x7fc721539d80(<=1)]>
Set the NSUserDefault NSConstraintBasedLayoutVisualizeMutuallyExclusiveConstraints to YES to have -[NSWindow visualizeConstraints:] automatically called when this happens.  And/or, break on objc_exception_throw to catch this in the debugger.

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