I did a bit more testing after applying the fix suggested by fmiyata (above). Things improved, but I get these notices in the "Reference" textarea at the bottom of the metabox when run with "define('WP_DEBUG', true);" in the wp-config.php file (I always run my test system this way). The notices are:
Notice: Undefined property: ShortcodeReference::$_url in C: ... \wp-content\plugins\shortcode-reference\lib\ShortcodeReference.php on line 183
Notice: Undefined variable: final_line in C: ... \wp-content\plugins\shortcode-reference\lib\ShortcodeReference.php on line 89
It doesn't matter which shortcode I click on; these notices always appear.
Below the notices is a link that says "PHP native" (all of the shortcodes say this) which goes to the http://www.php.net site. This seems inappropriate. Following that is the phpDocs information (which I put in all of my source code). There some minor formatting issues here, e.g., the return value for the "mla_attachment_list" shortcode is garbled.
The Shortcode reference idea is great, the presentation is good and I like the use of the phpDocs information. If there's anything I can do to help get this plugin working smoothly, let me know.