I have a similar issue, took me a while to nail it down to Custom Post Types UI but that definitely seems to be the cause.
Scenario: site under development with 3 Custom Post Types + 4 Custom Taxonomies.
Everything was working fine, with /%postname%/ permalink but somehow something happened, most likely after adding the 3rd post type.
Now the /%postname%/ permalink does not work, it results in most pages (normal pages, not posts - but strangely enough not all of them) going to the posts 'Home' page (not 404).
The 'default' permalink is working fine, so does the Numeric '/archives/%post_id%' permalink that I am using now.
I have tried different ways to correct this:
- not a theme issue: also happens with default WP theme
- not connected to another plugin as it also happens with all plugins (except CPT UI) disabled
- even moved a copy of the site to another server: still same issue
- archiving for CPT is on
- changed page names with possibly permalinks conflicting with CPT
- checked .htaccess file
I see that you are looking for beta testers for 0.9 version; could that version possibly address this issue ?