This recalls the situation you had a few months ago where one version of OS X reported file sizes differently from another version of OS X.
I'm suspecting that it's all due to how each file system manages things, and the overheads are different. Are differences generally proportional among large and small files, e.g., 1.01 times the size between systems, regardless of file size, or can you account for it by an offset that is more or less constant no matter the file size (would support the 2 versions of file name idea).
The real test is do the files "work" for each system? I'm guessing real time video might have a problem, but maybe nothing else. How critical is your work in this context?
Scott