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I'm having the same issue
started happening when I tried to manually rename multiple files and add extensions to extensionless files. Also - the folders I'm dealing with have several folders and files with extensive directory layers. I have repaired permissions, trashed com.apple.finder.plist, and restarted, which fixes the problem temporarily; however, once I start trying to rename files using the finder, I'm back to where I started.
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I posted this in another topic also - it seems that people have been having this issue a LONG time, over multiple systems, running different version of the OS.
here's the link to the other discussion - although it doesn't really answer the problem, at least we know it isn't isolated.
http://discussions.apple.com/thread.jspa?threadID=1299087&tstart=0
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