Thank you for the code 
I did try uploading it and seeing the output with my logic analyzer (don't have an oscilloscope with me).
AS you can see there are 3 breaks in this sweep.
The next one has no visible breaks in the sweep.
I am assuming these intermittent breaks are due to the prescaler being changed. Or do you think its an issue caused by my logic analyzer ans should not appear??
Is there a way to get smoother transitions?
Also is it possible to get the same complimentary wave in another pin 11? If so how would we go about doing it?