It ended up being bad data in some of the other records that were manually put in the file. I found that I actually had to remove the quotes from the eol specification in the dbh line and it worked.

Here's my code for the dbh line:

my $dbh = DBI->connect(qq{DBI:CSV:csv_eol=\n;csv_sep_char=\\~}); 
$dbh->{'csv_tables'}->{'JPDObj'} = {'file' => 'data/objectives-cqdc.tx
+t','col_names' => ["Obj","PosNbr","Year","Div","AVP","Dept","SDescr",
+"Major","Methods","Results","Accompl","JanUp","LDescr","Changes","Cha
+rs","Goals","Budget","CFObj"]};
[download]

-Jacvivus