Thanks for your message.
The details you provided helps us a lot.
We just figured out what is casing the problem and will fix it within the next release.
Its because you’ve PJHP 5.5 installed — It forces WordPress to use MYSQLI to connect to database and this is what is not CJT being support.
Check this: http://wordpress.org/support/topic/upgrading-to-wordpress-39-deletes-all-code-blocks — Its the same issue.
We will let you know once we got it solved.
You can get your local development server works if you can switch to PHP version before 5.5 or enable deprecated MYSQL extension if its being disabled by default.
Reply email from Ahmed (reposted by Damian to this forum topic)