I don't see why you need seek and tell at all.

open(FILE2,"<$file2name") or die "cant open $file2name for reading!\n"
+;

while ($A = <FILE1>)
  ($tmp,$pos)= split /\s+/, $A;
    local($/) = "";
    while (<FILE2>){
       @lines = split(/\n/,$_);
      ($posB,$posend) = findpos(@lines);
      next if $posA < $posB;
       last if $posA > $posB + $posend;
       processPara(@lines)
     }
    }
}
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Well, that's assuming the tell isn't really outside the while as it was in your code. And you never set $posA.

With those errors fixed, with the scoping errors fixed, with strict and warnings not disabled, with a better error message for open, and with proper indenting, we get:

use strict;
use warnings;

open(my $fh2, '<', $file2name)
   or die("Can't open $file2name for reading: $!\n");

while (<$fh1>)
    my (undef, $posA) = split(/\s+/);

    local $/ = "";
    while (<$fh2>){
       my @lines = split(/\n/);
       my ($posB, $posend) = findpos(@lines);
       next if $posA < $posB;
       last if $posA > $posB + $posend;
       processPara(@lines);
   }
}
[download]