I have this problem rather often. It seems that it happens more when I'm moving and altering large files. The more data I move around, create or delete - the more frequent and persistent the problem becomes. Typically a reboot fixes the problem. I'm totally unsure as to the cause (as I've got no processes that connect to empty folders ;-) ), but basically what happens is the folder or file will write itself as a "read only" file/folder and make itself immune to being changed. I suspect it's just a bug that windows has yet to address.

They'll probably just label it as a feature and call it some automated function. You know what they say, "a feature is just a bug with seniority."