This same problem is likely to happen with any Mac-to-Non-Mac file transfer, regardless of the method used to do the actual transferring. It is caused by the non-Mac dropping the resource fork. Last time I checked this was still a problem up to and including the latest version of Jaguar, as they all use some form of the resource fork. The only method for not losing the resource fork is to compress (tar, gzip, Stuffit, binHex, whatever) the file before transfer.
If you are storing mac files on a unix machine, you can get a little program called NetaTalk.
that will perserve the resource fork on the unix machine.
Also more info here
