NON-Printable Characters

I am running a collection of FMPro scripts and apple scripts to import a tab delimited text file twice a day. The first script runs and shuts down the database(to get past the record lock problem). Then the second copies the files from the server. The third then opens the files. The Problem: Sometimes the files that were updated show non printable characters. ( the square blocks ) And the strange part is the corrupt data is not contained within it's self. The fields that is linked to other files seem to be the problem. If I rerun all of the scripts (which deletes the files and puts new ones in its place) then everything is fixed.