Could it be that among those many rows and columns some of the data contains a comma? If that is the case your split just ain't going to do the job for you - you will get too many rows in the result and some of them will have too few columns.

You really should be using Text::CSV or Text::xSV to do the heavy lifting of parsing and generating CSV files.

Oh, and as an aside, always use strictures (use strict; use warnings; - see The strictures, according to Seuss).