Both problems are fixed, the new version will be available soon. Sorry it took a while!
OK so upon further testing, it appears that I am suffering from a random crash on loading character creation that is unrelated to this issue, as I can induce it independently. So scratch that off the list.
Additionally, I have also established that the problem is unrelated to UV changes/vert count. Basically the changes you introduced to fix the skin weight/node assignment issues in certain vanilla models now appears to cause that very same problem to occur in other models.
This one caused a lot of because its source was some code that I could have sworn I removed. Things weren't making any sense and I really had to do step-by-step debugging to find the issue. Bleh.
There appears to be a case sensitive issue where MDLEdit will not recognise the name of a node with differing case from the first instance, as per this example.
I glanced at that thread but missed your post somehow, thanks for reporting it here. The checks are now case-insensitive and the model loads properly.