I can't reproduce this one: I've had a couple vague reports of things like this, but I've never been able to reproduce it, so I suspect it's at least partially related to something in your server environment (e.g. text encoding?). If you can outline exact steps that will guarantee this behavior, then I can diagnose and fix it. Unfortunately
WP_DEBUG doesn't do much other than show simple PHP warnings and errors that any decent programmer should have fixed long before releasing a plugin.
Understand how WP handles post types: WP is totally oblivious to what's in its database. The only thing that puts a post-type on WP's radar is declaring it via the
register_post_type() function, so if your definition gets corrupted, then your post-types never get declared, and WP has no knowledge of them. There's a feature request to build out a detection tool/wizard that would help recover from this scenario (or migrate from some other plugin): https://code.google.com/p/wordpress-custom-content-type-manager/issues/detail?id=217 but I haven't needed it for any projects yet, so it hasn't been implemented.
There's functionality for exporting/importing your post-type definitions (see the CCTM->Tools menu), and it's a good idea to keep a backup of your definitions since recreating your post-types and fields can take a while.
As a last resort, check your
wp_options database table for the row where option_name='cctm_data' and see if you can read/salvage anything there. WP stores option data as a serialized string, which can be problematic and fragile and prone to corruption. Again, I've heard of this happening, but I've been unable to isolate the issue on any of my dev environments.