Apparently, the input file was corrupt in some way, perhaps loaded as binary instead of ASCII.
What we did: - pulled another file from the first server to the second server and tested - this one worked fine! - deleted the contents of this second file, and cut and pasted the exact text from the first file directly into this second file - ran the test again - it worked!
Everything, as far as we could tell, was identical between the two files. To rule out something to do with the filename, we then renamed this file to the original file's name, but it still worked. We then re-FTP'd the original file, and it worked this time as well. So, again, the only thing we can think of is that some non-printing characters were in the file.
We didn't have a hex editor available to check, but for anyone coming across this same thing, viewing the contents as hex would be one way to make sure there was nothing odd in the file.