Hi Patrick,
Check the following:
In the Player Template Builder, Layout tab, check the settings you have checked under Player Controls - do you have the "Display Forward/Back/Pause" checkbox checked?
In the Player Template Builder, on the Layout tab, in the Toolbar Menu, do you have the "Enable attachments tool" checkbox checked?
For the Notes button, check the Other tab and the Other section. Do you have the "Show slide notes button at bottom" checkbox checked?
The AP Help documentation
http://www.articulate.com/support/help/presenter/v5/ has information on all of the Player Template Builder features.
Hope that helps.
SFNancy