Why does CiviMail 'track click through' redirect to incorrect URLs?
Devin, your description is eerily similar to a problem I had on our Drupal site.  Without track click through, things were fine.  Once those were enabled, no dice.

For our situation (CiviMail - when Track Click Throughs is enabled, links result in a white screen with warnings), it turns out it was due to a PHP setting issue.  Jon G's answer explains the why.  Richard's answer explains how we fixed it.

Hope this helps!