As a complete guess, I beting that you are forgetting that we think of the first line of a file as being line 1, but thatthe first element of an array is (in the absence of deprecated useage) line 0 (zero).

In other words, if you want to read line 30 of the file, you almost certainly need to do

 tell FH, $lines[29], 0; $line = <FH>;

Another possibility is that you are forgetting to set $lines[0] = 0; and are instead doing

my @lines;  ## This should be my @lines = 0;
while( <FH> ) {
    push @lines, seek FH;
    ...
}
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Unless you push a 0 onto @lines, your first index position will be the start of line 2 instead of the start of line 1 and this will mean all your indexes are out-by-one from then on.