module_load_include fails on WebTestCase post
I figured it out for myself. This is an issue with SimpleTest. DrupalWebTestCase stores emails sent in the database, in a varialbe drupal_test_email_collector. If an email sent during a test case includes parameters, the parameters are saved. My parameters were classes. bootstrap.inc attempts to load and cache variables before modules are loaded. In restoring the emails with parameters, it was attempting to autoload the relevant class, and that was causing the crash.

This could happen, in principle, in other situations - any time a class got saved to a variable, though I have only encountered it with this test setup.