How to programatically add block to Drupal 7 page tpl AND respect visibility rules?
Turns out the solution was in how I was rendering the blocks.

Using this code to render my block added the block to Drupal's "knowledge" of the block being on the page.

$block = block_load($module, $bid);
$blockStuff = _block_get_renderable_array(_block_render_blocks(array($block)));
$output = drupal_render($blockStuff);
print $output;