First thing I noticed is that you split file 1 like so: 
($username, $firstname, $lastname, $lastlogin, $tokenexpiration) = spl
+it(",", $line);

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but the data looks like this: 
Alan,Bloggs,06/11/2009,11/30/2011

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meaning that $username is set to Alan, $firstname is set to Bloggs, etc.

Update: To avoid problems, I'd change your regex checking against the entire line ($line2 =~ /$lastname/ ... ) to something more precise. 
my ( $bs, $firstname_line_2, $lastname_line_2 ) = split (/,/,$line2);
if ( $lastname eq $lastname_line_2 && $firstname eq $firstname_line_2 
+) {
...

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In reply to Re: nested loops to compare 2 files is only looping a limited number of times. by Transient
in thread nested loops to compare 2 files is only looping a limited number of times. by stevemayes

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