WP's event-based architecture here is extremely vulnerable to conflicts. There's no pushing or shoving, you just have different actions registered to the same events, and there's always the possibility for unexpected behavior -- you don't know who gets to the party first. Given the limitations of the WP architecture, conflicts are impossible to avoid. I can't comment on the other plugins you mentioned, but understand that the CCTM alters a lot of the WP functionality, and sometimes very hacky approaches are required to keep the WP core from crumbling apart. This is one of the key reasons that I do not consider WP appropriate for production websites.
If you want to file a bug report, please provide the URLs of the plugins and the exact steps to reproduce the problematic behavior: https://code.google.com/p/wordpress-custom-content-type-manager/issues/list
No guarantee that these types of things can be fixed though.