First, I would suggest an entirely different approach, something like

while (<DATA>)
{
 next if /^\s+$/;
 my (undef,$pos,undef) = split;
 print "$pos\n";
}
__END__
BC001593 91 NPSL
BC001593 262 NASS
BC001593 293 NAST
[download]

Second, I can find nothing wrong with your regex above, which gives me the correct output when I enclose it in a loop similar to the one above:

while (<DATA>)
{
 next if /^\s+$/;
 my $sites = 0;
 if (/\w{1,12}\s+(\d{1,5})\s+[a-zA-Z]{4}/sm){$sites = $1}
 print "$sites\n";
}

__END__
BC001593 91 NPSL
BC001593 262 NASS
BC001593 293 NAST
[download]

Therefore, I suggest that there is something wrong with your looping structure, rather than your regex.

I hope this helps.

--
Regards,
Helgi Briem
helgi AT decode DOT is