Panels template files: Inheriting a tpl file in a sub theme
Here's the weird news, just having a panels-pane.tpl.php in a parent theme should work. It's working for me in a highly used parent theme. So I'm guessing any theme suggestions or other steps aren't going to cut it...

I would check for typos, in this case I would look at the file name (sounds like that's fine), then I would check the sub-theme info file to make sure that's set correctly (although it sounds like that may also be right)

base theme = base_theme_name


Then I would check file permissions on tpl/theme folder. 664 tends to work for me, and apache needs access to it and the folder it's in.

If that seems fine my two steps before I panic with drupal are:

drush rr


restart apache

Hope that helps.