First rule of fixing broken perl code. Apply 'use strict;' and 'use warnings;'. This gives a lot of warnings and errors with your code, which would warrant sorting first.

It looks like you're doing a fairly substantial number of slightly horrible things. I would imagine that if you did use strict and warnings, your problem would vanish (or become obvious. For starters - populating an array by setting $n.

my @jobvar_list = ( "senior", "exec" );
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Will do exactly the same thing. Even better, you could use a hash, so you never needed to iterate through one list, and reference another list.

my %jobvar_list = ( 'senior' => 'Senior',
                       'exec' => 'Exec' ); 

my $quick_jobtype = "exec";
foreach my $temp_jobvar ( keys %jobvar_list )
{
  print "$temp_jobvar, $jobvar_list{$temp_jobvar}\n";
  if ( $temp_jobvar eq $quick_jobtype )
  { 
    print "$temp_jobvar matches $quick_jobtype";
    my $sortby = " WHERE jobtype like '%$jobvar%' and active='yes' AND
+ jobstatus!='suspend' ORDER BY dateadded DESC, jobtitle ASC";
    print $sortby;
  }
}
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I think it must be that 'if' clause that's causing you problems - what is it trying to do? It sounds like it's evaluating but never working, and therefore not running that 'sortby' and 'Build_Lists_Both' segments of code. Which is odd, because it seems to be doing so in that sample code you posted. Is there any chance that you've tidied your code up a bit, with the job title list? that 'eq' line means that the two variables have to match precisely - no whitespace or linefeeds. Because your code _does_ run as is.