RadFormDecorator is implemented in such a way that it will not style controls that have a CSS className explicitly set. In such cases it "assumes" that the developer has chosen to take care of the styling.
This *separation* is made because very often it is not possible to mix the CSS injected by the form decorator and the developer together - there are many negative side effects.
Whether the decorator is on a master page or not - it will behave in the same manner. There are no master-page specific issues.
If you are not able to resolve the issues, my suggestion is to send us a running project that demonstrates those, and we will do our best to solve the visual problems. Sending us a MS Word doc with screenshots of the observed problems will be helpful too as it will allow us to focus on those immediately.
the Telerik team