Thank you for your post.
I wasn't able to recreate the issue you're having. Are you using the latest version of PlusSpec (v17.2.0)?
The Rafter Tool was optimised for hip roofs but should still work for most skillion roof designs. What I would recommend to do if it doesn't work correctly is to use either the Ceiling Joist/Rafter/Purlin Tool, Beam Tool, the option in the 'Advanced' section of the Rafter Tool or a combination of all of these. Would you be able to please let me know if this works for you?
If it doesn't work, would you be able to please send the model across to email@example.com
so I can look into is further?