File sizes the same?
If you're right, and 'mode' is OK, I'd start checking the connection paths. Remember, for example, the FTP is a "dual-channel" protocol, and make sure that both channels are working.
And, while we're at it, when you say 'mode', you mean 'passive' vs. 'active' ... 'cuz what you're describing sound awful similar to binary/ASCII issues ... but you probably already knew that.... 🙂