File contents switched on transfer

Everything seems to upload/download just fine but if I look at the files, the contents of the files has been switched. It's almost like the files get the wrong names associated with them after transfer.

File A - Contents A
File B - Contents B

After transfer:

File A - Contents B
File B - Contents A

The ftp is between a Windows 2003 Server and Windows XP (same on Windows 2000) client.

It seems to be a problem not with SmartFTP itself as I've seen the same issue with CuteFTP.

Anyone else encounter this issue? I'm hoping someone has and already figured it out. :>