I guess that you are trying this with a file that has been generated on Windows and then transferred to a UNIX box. You end up with extra ^M chars when you look at the file using vi. Try trimming the surplus whitespace using a regex 
#!/usr/bin/perl -w

use strict;

while (<MYFILE>){
    s/\s+$//;
    if (/NEXT LINE MARKER/) {
        my $nextLine = <MYFILE>;
        $nextLine =~ s/\s+$//;
        print "$nextLine\n";
        # do stuff with the next line here.
    }
}

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In reply to Re^3: Matching string, then getting next line by inman
in thread Matching string, then getting next line by minixman

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