I'd have to see more of your code to be sure, but if you're using a global %data, you'll definitely run into clobbering problems, because you're assigning a reference to the *same* hash each time. You can take two approaches:

while (<DATA>) {
    chomp;
    my @fields = split(/$sep/, $_);
    my %data;
    @data{@fieldnames} = @fields;
    push @datalist, %data;
}
[download]

Or:

while (<DATA>) {
    chomp;
    my $data = {};
    @$data{@fieldnames} = split(/$sep/, $_);
    push @datalist, $data;
}
[download]

I'd choose the first, as it's sometimes tricky to get at lists from hash references, and it's more clear. I would get rid of @fields, though, as it's a synthetic variable.

The trick here is making sure you have a new lexical %data each time. Just a guess, but it's bitten me a few times.

Update: Yes, the push line in the first example should use \%data. That'll teach me to get up early.