|Do you know where your variables are?|
>> ftp usually starts up in ASCII mode
As I said, my experience has been that ftp usually starts up in ASCII mode. I believe that some ftp daemons can be configured to default to binary mode. Since most of the traffic is likely to be binary, doing so would make a good deal of sense.
>> Perhaps the files were in a .tar or a .zip?
From the way Ovid's original post was worded, it didn't seem so.
>> Would there be a similar problem when moving Perl files en masse from *nix to Windows?
Well, I know that text files can lose their end-of-record markers, turning a multi-line text file into a very long single line. I don't know whether Perl's parser will recognize \n vs \r\n as an end of line marker. It may, which could result in a perfectly valid Perl program that looks like a very long one-liner.
At that time  the chief engineer was almost always the chief test pilot as well. That had the fortunate result of eliminating poor engineering early in aviation.—Igor Sikorsky, reported in AOPA Pilot magazine February 2003.