First, please read How (Not) To Ask A Question and Markup in the Monastery, since you have not really provided us with the input you are really consuming and you have not followed site protocol in terms of appropriate mark-up.

I note that line 6 of the code you gave us, you are assigning a list to a scalar. This will result in only the first value being stored in your hash of hashes and the second being put on the rubbish heap. Perhaps you meant to use square brackets to make it an anonymous array reference (see perllol).

Given that your stated intention is just to sum up the associated values, you certainly do not need a data structure as complex as the one you have used here. You need only use a simple hash, keyed on your KEYIDs and accumulate values using += (Assignment Operators). Something like this, perhaps:

use strict;
use warnings;

my %baldata;
while (defined(my $line = <DATA>)) {
    next unless $line =~ /^FB/;
    my ($key,$value) = split /\,/, $line;
    $baldata{$key} += $value;
}
foreach my $key (keys %baldata) {
    print "$key => $baldata{$key}\n"
}

__DATA__
ID,Value
FB208025,1629.01
FB208025,1201.16


FB091027,1257.66
FB091027,741.92

FB135022,11210.66
FB135022,3238.67
FB135022,3569.34
FB135022,5534.23
[download]

Note that, of course, the above code will not work with your original file.