I think I'll keep it on auto.

But it may be the auto setting that's causing somefiles to be corrupted and others not. The only thing I can think of that could be the basis of a decision for it would be file extensions, and it might be seeing some as text and others not.

do you think Ultraedit will, in fact, solve this

It should at least mask it to the point where no one cares. I assume that the text files are only used on the Unix side. Keep in mind that many Unix programs that expect text files will not read them properly if they're not in Unix text file format. Some will, though. So if you see odd things happening, then non-Unix text files may be your problem.

So, do you think Ultraedit will, in fact, solve this? Or do I have to save the files in a Unix format?

To take a step back, the way that Ultraedit could solve the problem is by saving the files in Unix text format. But, I'm sure, you'll have to make sure that each file you create is in that format. (It'll probably retain the format for existing files unless otherwise told.) It seems to me that setting your FTP client to do the proper translation and keeping the text files in their native formats on each given platform would be easier.