Are you using TotalFinder or PathFinder? There is another thread where others saw this caused by those programs. However, I think some saw the problem without those.
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I'm having this problem, too. I'm also using TotalFinder (to restore something akin to the old label function -- still frustrated with Apple for thinking that "tags" have the same function), so I'll share this thread with their development forum in case the problem is tied to TotalFinder.
While it's annoying, it's also somewhat benign -- it just means relaunching periodically. But with Mavericks still crashing regularly, I'm doing that anyway... 👿
Mavericks leaves phantom mini-windows on my desktop?