FTP servers and clients exchange some OS information at connection time; if their OSes match they will default to "binary mode" (8-bit wide transfers) and if not they will fall back to ASCII (7-bit).
So linux machines will automagically use binary modes with other *nix type operating systems, unless you have specifically configured them to do otherwise. It's only with dissimilar operating systems (for example, liux & windows, or windows & MVS, etc.) that this problem comes up.
I know that's not really answering your question, but I thought you might like to know why it sometimes defaults to binary mode and other times does not.
As the previous poster noted, you should have a configuration file somewhere for your ftp client; if it is possible to override the mode that's probably the best place to do it.