Got a response from Atmel about my issues using Atmel Studio 6 trying to implement the ASF wizard with a C++ project. It was working with C projects but not C++/ Trying the below solution fixed this. Have yet to upload the code aand probably wont have the opportunity for a while still. At least it compiles nicely now with all the files.
You can create a C++ project by opening Atmel Studio 6.0->File->new->project, click C/C++, select GCC C++ Executable Project, then choose the device you use.
Unfortunately, ASF wizard does not support C++ project yet. You can copy source files from a C project or use the following workround:
1. Right click on the project in the Solution Explorer and unload it.
2. Right click on it again and choose edit *.cppproj.
3. Change the <Language>CPP</Language> tag to <Language>C</Language>
4. Reload the project. Now you can add with ASF wizard. But, it is to be noted that only C compiler will be used with this.
5. So, repeat the first two steps and change <Language>C</Language> back to <Language>CPP</Language> and reload the project.
Now, it will work as a C++ compiler for the build.
Hopefully this will work as I progress through the code :)