I had a similar problem on Win98, using perl through cygwin. It turned out that somehow, someway, it was interpreting some of my data to be printed as escape sequences, and deleting surrounding text. Instead of printing :
"The number 123 goes here." It would print
"Th23 goes here." (Or something like that.) The number was a 12 digit UPC that was joined together, so maybe it's the same problem. I got around it by not printing it at all. Good luck.