I don't know what the heck the user invented on this one (God, how I love the users! ..lghs) but, when I save it as '.txt tab delimited', I see many of those black squares in between the text.

Is it what you called 'corrupted'? Your description sounds like CRLF (\r\n), this is what considered as newline character in OS such as Windows. Try to clean the string with s/\r//g. But this normally doesn't make the process hang. Well, out of all, MS applications are notoriously known as 'weird characters inventors' at their best.

I once read about how to get rid of these funny stuff MS applications introduce but I can't recall it at all. The person(s) that made this stuff did it by reverse engineering how MS Excel works.