Many people have complained about spurious "Metadata file needs to be updated" icons appearing on thumbnails in Library mode. That has happened to me off and on for a year with LR 3. I now have a small 16-image catalog for which this happens repeatedly. No matter how many times I select all the thumbnails and do Metadata > Save Metadata To File, the needs-updating icons reappear very quickly, usually within seconds. The metadata is getting written to the files correctly -- it's just that LR doesn't think it has.
The test catalog was created with LR 3.5RC on Windows 7 by exporting from my main catalog (also exhibiting the problem).
Adobe, you can download the zipped folder containing the complete catalog and images from: