Squeeze Problem (version 4.5.7 on Tiger)

Some of our filenames get pretty long. However, they are way under the 60 character limit of QuickTime. According to Sorenson's website, the only limitation enforced is the one by QuickTime. But, when we name something 28 or more characters long, Squeeze renames them by shortening the name. The end result is that everything in folder gets renamed that has the same root name. If we add the files individually, we don't have this problem. It's only when we add a whole folder that this happens. Anyone else seen this? Wondering if there is a fix.