When I run the loop as ... it outputs data appropriately ...

I doubt it. Just to drive home the point of jethro's reply above, consider:

>perl -le
"use warnings;
 ;;
 $empty_string = '';
 @ra = split ',', $empty_string;
 ;;
 $foo = $ra[3];
 $bar = $ra[5];
 print qq{'$foo' '$bar'};
"
Use of uninitialized value $foo in concatenation (.) or string at...
Use of uninitialized value $bar in concatenation (.) or string at...
'' ''
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And once again, do yourself a favor and  use warnings; and  use strict;