I'm afraid I cannot replicate your problem. Running Perl 5.6.1 under Windows NT, the following code:

sub dec2bin {
    my $str = unpack("B32", pack("N", shift));
    $str =~ s/^0+(?=\d)//;   # otherwise you'll get leading zeros
    return $str;
}

sub bin2dec {
    return unpack("N", pack("B32", substr("0" x 32 . shift, -32)));
}
print bin2dec("101")," ",bin2dec("111"),"\n";
print dec2bin(5),    " ",dec2bin(7)    ,"\n";
[download]

..produces:

5 7
101 111
[download]

..exactly as expected. Perhaps you could show up some of the code that attempts to use these functions? Or perhaps I'm misunderstanding you when you state you "get the exact same binary out."

 
perl -e 'print "I love $^X$\"$]!$/"#$&V"+@( NO CARRIER'