[elzr]

I'm also quite smitten with Pixelmator: it's full-featured, robust, cheap, fast & native! For my purposes, I honestly prefer it to the much clunkier and much more expensive Photoshop.

Have you tried using Pixelmator actions in Automator to replicate pixel-precise cropping? See http://imgur.com/nDTcxvS I recently processed hundreds of screenshots this way and it worked well.