actually I did not.
I was lucky that in all installations where i used CCTM I never needed hyerarchical custom post types.
the only website where I had hyerarchical CPT I needed child posts just for admin purposes and using Mike's solution fixed the parent posts... so this issue was not really harmful.
I've read your post and I'm sure I will use your workaround if I'll need to build a hyerarchical CPT. When I'll do I'll surely post a feedback in this thread.
I'm quite sorry that fireproofsocks does not have the time to fix this issue, because even if there are others super-awesome plugins for managing Custom post types (free or premium it's the same, I don't really bother spending some bucks if the tool saves my time), I still prefer CCTM because it's not invasive and can be coupled with a lot of other plugins or custom code.
For example: I use very often CCTM to build custom post types but another one (Advanced Custom Fields) to manage custom fields. Never had a problem! All plugins should be granular, I hate the "all-in-one" trend of premium plugins!