It looks to me as though you've got your 'resume' condition (the fifth field has an end-comment marker) inside the condition wherein you detect a start marker. This means that you'll only skip the first line after a start marker. I don't see a straightforward way to avoid checking the fifth field every iteration.

How 'bout something like this (untested):

my $skip = 0;
LOOP: while ($line = <CMDTXTF>) {
   @fld = split /\|/,$line;
   if ($fld[5] =~ / \*\//) {
     $skip = 0; 
# you found an end-comment, turn skipping off for the next line
     next LOOP;
   }
   if ($fld[5] =~ /\/\*/) { 
     $skip = 1;
# you found a start-comment, turn skipping on
     next LOOP;
   }
   unless ($skip) {
     print "$fld[0] $fld[2] sequence=$fld[4] $fld[5]" if $line =~ /$re
+gexp/;
   }
}
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