Based upon your update, I would say dHarry's diagnosis that you have unaccounted for newlines is correct. One way to fix that would be:

open PL, 'pvclength.txt' or die "Cant open file";
$pvc_l=<PL>;
chomp $pvc_l;

open GIL, 'gilength.txt'or die "Cant open file"; 
$gipipe_l=<GIL>; 
chomp $gipipe_l;

open QGBS, 'qgibendsocket.txt' or die "Cant open file";
$gibend_sck_q=<QGBS>;
chomp $gibend_sck_q;
[download]

See chomp.

You also mention in your OP you "tried removing whitespace from the Qty variables". How? What code did you use? This should be straight-forward using regular expressions.

Please note that because all your variable names are different lengths, your columns will not align - you have a different number of spaces following each one. Again, a simple solution is to follow dHarry's advice and use sprintf.

Also, note you dropped a sigil off of pvc_l in your OP. Please get in the habit of testing code before you post so Monks don't go off chasing red herrings. See How do I post a question effectively? and make sure posted code passes strict and warnings.

Update: Fixed oversights in code. Thanks wfsp.