The issues you're talking about aren't ones I've seen anyone else complain about (and don't happen for me), so I'm wondering if there's something specific to your configuration that's affecting it.
Disabling transparency in the accessibility options used to fix it, but it doesn't anymore.
I'm very much hoping that Apple will include this functionality in the next major release of OS X as f.lux has historically had trouble keeping up with OS and hardware updates.
Thanks for that useful comment, man.