One error I found was the last sequence wasn't being added to the %protein hash. You need to add it at the end of the while loop.

{
open (IN, $file) || die "Can't open $file\n";
my $tag; my $seq;
while (<IN>) {
  chomp;
  if (/^>/) {
    if ($seq) {$protein{$tag} = uc($seq); undef $seq}
      $tag = $_;
    }
  else {$seq .= $_}
  }
$protein{$tag} = uc($seq); # add this line to get the last sequence
close IN;
}
[download]

With a few other adjustments, I was able to get the script to run. However, I don't know what changes need to be made to get accurate results.

With an inputfile of:

>chr1 RecName: Full=Putative transcription factor 001R;
MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPS
EKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLD
AKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHL
EKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDD
SFRKIYTDLGWKFTPL
>chr2 RecName: Full=Uncharacterized protein 002L;
MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASGFCTSQPLCAR
IKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADLIDTQAQVDQFVSMFGESPSL
AERYCMRGVKNTAGELVSRVSSDADPAGGWCRKWYSAHRGPDQDAALGSFCIKNPGAADC
KCINRASDPVYQKVKTLHAYPDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNML
DDGSVTMDDVKNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRK
VMFFVAGAVLVAILISTVRW
[download]

I got results from your program below

>chr1 RecName: Full=Putative transcription factor 001R;    9.425903320
+3125
>chr2 RecName: Full=Uncharacterized protein 002L;    8.2193603515625
[download]

These results vary from a program I wrote using Bio::Tools::pICalculator. The results I got from it were:

chr1    9.793558
chr2    7.791410
[download]

That program code was:

#!/usr/bin/perl
use strict;
use warnings;
use Bio::Tools::pICalculator;
use Bio::SeqIO;

@ARGV == 1 or die "Usage: perl $0 fasta_file_name\n";

my $in = Bio::SeqIO->new( -file => $ARGV[0] ,-format => 'Fasta' );

my $calc = Bio::Tools::pICalculator->new(-places => 6);

while ( my $seq = $in->next_seq ) {
     $calc->seq($seq);
     my $iep = $calc->iep;
     print join("\t", $seq->id, $iep), "\n";
}
[download]

I got the code from the documentation for that module.

Chris