Well. Having looked at it scientifically on a Saturday afternoon the problem is solved.
I went through and recorded some sin waves to have a look and changed some settings as I went. Turns out the headphone output was a red herring and exactly the same as the rest.
A combination of Phase init set to 1 and Punch set to 0 have solved the problem. Last week I must have been doing each of these but never both together. (the init patch I have has punch set to 64 and phase init set to off.)
Thanks again for your thoughts and help. Now I can get some Elektron A4 fatness with Virus as sine sub.