Can't transfer JavaScript (.js) files with any FTP program in Vist

This is just one of my problems. I have Vista Ultimate installed on my pc at
home. I'm a web developer and I routinely use ftp programs (generally
Filezilla but I've used others with this problem) to transfer files from
other web servers to my pc and then back again. However, every single time I
try to transfer a javascript file with an extension of .js the file errors
out (I can't remember the error I get).

If I temporarily change the extension to something other than .js it will
transfer just fine but then I have to remember to change it back. If I'm
transferring just one javascript file it's not that big of a deal but
sometimes I transfer a whole folder with it's subfolders and it's a major
pain to have to first go through all of the folders and subfolders, change
the extensions on all of the javascript files, transfer the files and then
hope that when I'm going back through the folders I don't miss changing one
of those files back to a .js extension.

Does this problem have something to do with the Windows Vista firewall? If
so, how the heck do I fix it?

Thanks