I have noticed that problem. Also, if you set a filter (such as Normalize), it won't do that either.
Nero Burning ROM will show that the settings such as pause and filters have been made....but after burning the CD, the windows return showing your tracks and all settings are reset back to the default.
I sent Nero an email about the problem, and they wanted a list of error messages generated. Well no error messages were dispalyed. The CD burned....but without my specific settings. I tried to tell Nero that, but I don't think they understood.