This is one that's got me very confused.
I have a site which is using the free version of Traction. I have some Custom Post Types and Custom Taxonomies. I have files called taxonomy.php and single-CPT.php and everything works perfectly, no problem at all.
I want to change the design, and am using plaintextblog (oldie, but goldie) as a base. I recreate my taxonomy.php and single-CPT files and they get ignored. All single posts are displayed using single.php, post-listings use index.php.
[I stick comment tags at the top of my template files so I know which one has been pulled in. Wish theme developers did the same.]
All the CPT and CT code is in a separate plugin file, as I'm using a different template for touch devices, so it's not that i've forgotten to copy the CPT/CT code over. If I rename taxonomy.php to index.php it displays correctly, so the file isn't corrupted.
What's confusing me is that the template hierarchy indicates that taxonomy.php should be pulled in if it exists (even if error-strewn), no extra code required - and WordPress isn't doing that. If I read the Template Hierarchy page on Codex correctly, it's even ignoring archive.php. I've used plaintextblog as a base to a different theme on another site, and CPTs/CTs work fine.
What might I be missing? Help me Obi-Wan, you're my only hope.