I have a function that takes an image, resize and crop it, and save it as normal, then resize it again and crop it again to create the thumbnail. The numbers of the second crop were WAY off, and the calculations were perfect, the problem, was the second crop wasn't resetting the imagePage, so if you try to crop the same image twice, it will be a good idea to reset it first:
<?php
$thumb = new Imagick($file)
$thumb->resizeImage($r_w1,$r_h1,Imagick::FILTER_CATROM,0.9, false);
$thumb->cropImage($w1,$h1,$l1,$t1);
$thumb->writeImage($destinationPath.'/'.$fileName);
$thumb->resizeImage($r_w2,$r_h2,Imagick::FILTER_CATROM,0.9, false);
$thumb->setImagePage(0, 0, 0, 0);
$thumb->cropImage($w2,$h2,$l2,$t2);
$thumb->writeImage($destinationPath.'/'.$fileNameThumb);
?>
BTW, i needed perfect dimentions so i had to set the "bestfit" to false.