We have been seeing issues with 6.0 patch not working, means not fixing the issues that it is suppose to. One possible cause is that, some of the cache data are not cleaned up that causes the patch not to work properly. Here are the steps to fix.
1. Close all opened studio instance.
2. Disconnect any devices (atmel debugger, tools) connected to the computer.
3. Go to <Atmel Studio install directory>\avrdbg, delete the folder by name codeCache.
4. Now install the patch.
5. Launch studio, and things should work ok.
Have a good time with studio.