I've set up my site with Drupal 4.7RC3, and have installed the Taxonomy Themes module. I'm basically setting up the site as a blog, but with a Music section that lives under 'taxonomy_menu/4*'.
I'm using the Meta-Theme theme, which is based (i think) mainly on CSS, as it has a bunch of CSS variations (meta-grey, meta-pink, meta-black, etc). What i'm doing is: using Taxonomy Theme, I set everthing under (and including) 'taxonomy_menu/4*' to use the meta-black theme, and everything else to use meta-grey. That is all well and good, and works fine, but other than using different themes for the two sections i want in my site, i also want the two sections to have different block setups. So, i go into the block administration and set the blocks that i don't want to show up under 'taxonomy_menu/4*' to not show up there, and the ones that i do want to show up, i set to show up only under 'taxonomy_menu/4*'.
The thing is that these block rules are obeyed if i don't have Taxonomy Theme enabled, but not if I do (I mean - they're obeyed everywhere except under 'taxonomy_menu/4*'). Not only that, but when Taxonomy Theme is enabled, not only are block rules not obeyed under 'taxonomy_menu/4*', but some blocks that aren't even enabled in the blocks configuration show up (eg - "Browse Archives" block - even though it wasn't enabled, I had to specifically set it not to show up under 'taxonomy_menu/4*' ... a rule which is obeyed with Taxonomy Theme enabled!?)! A self-created block (to display last.fm feed) that i want to show up under 'taxonomy_menu/4*' just won't (unless i disable Taxonomy Theme).