Url aliases/global redirect not being used in Custom Blocks This one's weird.  Drupal 7.

I have a complex front page - lots of Views, also lots of custom blocks using code I wrote from scratch - functions that essentially query the database directly and output different lists of content.

For some reason, these custom lists aren't using the generated url aliases.  They just link to node/#####.  Further, Global Redirect isn't working for them either.  What gives?  

To see in action: http://www.ainonline.com.

You'll see most of the top stuff has the generated aliases.  The ones in the middle towards the bottom, under the individual channels, use the system urls.  Any ideas?
Found the answer.  Sort of surprising since I don't think it's uncommon to run Drupal from a subdirectory (im my case, "drupal") and hide the fact through .htaccess rewrites.  Anyhow, doing exactly that breaks Global Redirect.

The fix is unfortunately hacking the module until it's addressed.  See here:
http://drupal.org/node/976214