I don't have a fix for you, but instead I'm offering some refactoring advice.

1. Load what you need from the annotation file into a hash.
2. Might as well do your processing one line at a time, no need to have the whole file in memory.

Here follows some code to implement these first thoughts. I have not changed your use of the global @window, @probe, which would be my next targets for refactoring. But I think after you refactor, you may find it easier to debug.

open my $annotation_read_handle, '<', $annotation_file;
my %annotation_for;
while (my $ad = <$annotation_read_handle> ) {
    # read $an_chrom, $prol, $pror out of $ad
    my (
        $an_chrom, undef, undef, 
        $prol,     $pror, undef, 
        undef,     undef, $mess,
    ) = split(/\t/, $ad);
    # read $name out of $mess
    my (undef, undef, $name) = split(/\;/, $mess);
    
    # store for future lookups
    $annotation_for{$an_chrom} = [ $name, $prol, $pror ];
}

# loop through the main data file
OLC: 
    while (my $md = <$main_read_handle> ) {
    # remove newlines
    chomp $md; 
    # pull out chromosome #, window start, end
    my ($main_chrom, $winl, $winr) = split(/\t/, $md);
    # see if $main_chrom has been annotated
    next OLC if !exists $annotation_for{$main_chrom};
    
    my $array_ref = $annotation_for{$main_chrom};
    ( my $name, @probe ) = @$array_ref;
    # put the window start, end into array for further processing
    @window = ($winl, $winr);

    # call the range_finding sub to look for matches
    my $return = range_find();
    next OLC if !$return;
    # upon matching, print out the name of the gene along with the ori
+ginal values
    print OUTPUT "$name\t $md\n";
}
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