Correct, the issue is caused because the plugins (Image Source Control and Twitter Boostrap CSS) are including pluggable.php before wpDirAuth is loaded, there by defining wp_authenticate and wp_setcookie before wpDirAuth has the ability to. The functions in pluggable.php are specifically written to have the ability to be overridden by plugins. A plugin that loads this file hijacks the ability for any other plugins to override any of these functions.
The situation isn't unique to wpDirAuth: any plugin that needs to overwrite any of the functions in pluggable.php that load after one of these plugins (e.g. ISC) will not be compatible. The situation is just worse for wpDirAuth because plugins are loaded alphabetically and 'w' is at the end of the list.
I'm working on a method that will reduce some of the reliance on overwriting wp_authenticate (even though the wordpress plugin structure was written specifically for authors to over ride the functions in pluggable.php), but these other methods are introducing other conflicts. I guess the other option is to do plugin-loading hacks to make sure wpDirAuth is loaded first, or maybe rename it to aWpDirAuth so it's higher in the alphabet. o_O
@Webzunft, wpdirauth is a niche plugin that allows wordpress to authenticate its users against LDAP/AD instead of local user accounts. It was actually updated last November so not quite a year. Also, considering it is a niche plugin, it is actually quite popular with over 14K downloads. ;)