I have an example with repeatable behaviour for you that demonstrates that mutate will choose worse scoring sidechains from a given position and keep these worse scoring sidechains, even when CL=1. It got to these better scoring ones using mutate to begin with !
This to me sounds like undesired behaviour.
the file is in the contenders group solutions for puzzle Sepsis 2 and called 'will_mutate_badly'.
My client is 2012-09-21-51299M-win_x86-devprev.
This is something that has not been picked up, but could be influencing other bugs for 633 for example.
I am amazed that such a core function would be left without attention for days.
I am boycotting any puzzle that relies on mutates, effectvive today.
This isn't a bug; mutate is working as expected as far as I can tell. That solution has a band in it. When bands are present, the score may decrease as the game will try to satisfy the bands at the expense of score. If you disable the bands in that solution, mutate will only increase the score.
Thank you Seth, I missed the band. I apologize for having caused waves and eaten your time.