Andy,
Have you opened the offending file in Notepad to see what's going on?
I've had a similar issue with Rhumba 2000's data file transfer. This program brings data down daily into a text file. It appearantly does not put a line feed after the last data downloaded. If a second days' data is appended to the file, the first caracter of the second download appears to the right of a CR like character on the last line of the first download and fouls my dts package.
The only thing I can think of, is to put the file through a pre-process that would loop through the file and if the length of the line is greater than x characters dump the extra data into your own log file. If you're having the same trouble I am where lines are doubling up, this process could break the long line into two lines. It's also possible that your field definition may need to change.
Good luck,
John