Not sure why yet, but if you use the CSV file, the last line is ignored.
Workaround... put a dummy last line.
Edit: I had a malformed line in the file with an extra ,
This code caused the problem (well sort of)
Code:
$bop_find_array = array_filter($bop_find_array);
$bop_find_array = array_values($bop_find_array);
$bop_replace_array = array_filter($bop_replace_array);
$bop_replace_array = array_values($bop_replace_array);
The two arrays ended up with a different number of elements.