I've figured out the problem,

I'm glad for you! :-)

and it has nothing to do with DBD::CSV.

I'm glad for me! :-)

Of course, if there's a nifty setting to handle unescaped quotes, I'd be glad to learn of it!)

Are the fields already quote delimited? In other words do they resemble number 1 or number 2?

   1. "foo","bad " bad","bar"
   2. foo,bad " bad,bar   

If you have records of type #1, I don't have much to suggest beyond the pre-processing you are already doing. If your records are of type #2, however, you ought to be able to handle that all within DBD::CSV. Set csv_delim_char to undef, in which case the stray quote will not be an embedded delimiter, it will just be a quote because you will have set the delimiter character to be undef rather than double-quote. If that won't work, show us some data and maybe someone will have a suggestion.

Thanks for following up to let us know how it turned out.