Well, I got tired of staring at the error so I just fixed it myself.. Not sure if this is a hack, (it may be fixed in SVN or something).
What was happening is that the plugin array was being filled with both the directory path and the file path for each plugin activated.. So even though your plugin would run the include_once would also fail on the directory call.
To fix this just replace line 582 of wp-settings.php with
if ( is_file($plugin) && '' != $plugin && 0 == validate_file($plugin) && file_exists(WP_PLUGIN_DIR . '/' . $plugin) )
All that I added is the is_file() check to be sure that include_once is trying to include a file and not a directory. The array should be fixed, but this will do it for now.