I have tried to reproduce this on Sitefinity 4.4 so I can better advise you why this is happening. The steps tested are:
1.Create new template
2. Base the new template on another template
3. No draft have been created, the "Base on template column in the templates grid was filled with the template I selected"
Can you elaborate on the steps a little more of I have misunderstood them?
I have tried the steps mentioned the way I interpret them might be different tough. I create two master pages one is standard and teh other is nested master page. I create new template with the base master file and teh template is called "A". Then create new tempalte "B" with the nested master page file. I don`t select the option base on template and all is running fine.
The problem still exists in 5.4
If you want to create a new template from a .master and you have not set any other template to be used as default, Sitefinity will create two templates.
You need to have a template set as default to create your own template from .master correctly.
Is there a PITS for this?