Don't rule this a bug in DBD::CSV until you do more investigation. It is quite possible that there is a single mis-matched " in the file, and DBD::CSV is interpreting that oddly, and you lose lots of lines. Try taking the CSV file and cutting it in halves, see if each half is handled normally, and then do a binary search to find the data confusing DBD::CSV. After you find that, then decide whether it is doing the wrong thing, and if it is, then you can now send a useful bug report.
If there is a data problem, running through the file with Text::xSV might spot it very quickly since it doesn't try to DWIM around errors and gives fairly detailed error reporting.
As for your code, you do not handle commas, returns or double-quotes properly in a quoted field. Doing it right is surprisingly tricky. I would suggest using a module. Here are some options. Text::CSV is simple to use, but doesn't handle embedded returns properly. Text::CSV_XS is much faster and does handle embedded returns, but it has to be compiled. Text::xSV also handles embedded returns, but is much slower. Unfortunately no two of these have compatible APIs.
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