The most common reason that files are not grouped together despite all outward appearances placing them as 'the same' are that the actual SHA1 hashes are different. LimeWire uses a very secure hashing scheme (very much unlike the insecure Kazaa scheme) that changes even if a single byte in the file differs. The sizes and names be the same, but some type of meta-information within the file may have changed (such as ID3 tags on mp3s, or other information for other files) causing the hash to be different.