Came across this issue, and don't know if it's a Drupal 7 issue or a Zen issue so I thought I would post it here.
I have a Drupal 7 site, and in the future I plan to have a couple of related sites on the same domain so I am using Drupal's multisite. So I have the normal sites/all/themes dir and a sites/outliersolutions.com/themes dir.
I almost always use Zen for my base, so I thought I would put the Zen theme in the sites/all/themes dir and then have my sub theme in the sites/outliersolutions.com/themes dir. This worked fine for awhile, then I ran into some problems with template overrides.
Namely, while my page--front.tpl.php and a view-field override worked just fine, I could not for the life of me get any other page or node overrides to work. Specifically, I wanted to have a custom page or node tpl for my 'philosophy' page, which was node 3. I tried node--3.tpl.php and page--node--3.tpl.php and neither would work. I was clearing my cache, theme reg was set to clear each time, and I made sure to have my node.tpl.php and page.tpl.php files in same dir as my overrides (sites/outliersolutions.com/themes/onepointtwentyone). Nothing worked. Then I thought, I'll try moving the Zen theme folder out from the sites/all/themes and put it in the sites/outliersolutions/themes dir. BAM! Everything worked fine.