Yes, this is more a chemistry question, but that's fine by me anyway. The mods might want to move it to the 'chemistry' section though.
I don't quite see what you mean. More specifically, I don't see any particular relationship between 'chemical clock' reactions and entropy as compared to any other chemical reaction.
Are you sure you're not conflating entropy, which is often equated with disorder, with chaos, which is a behaviour of dynamical systems exhibited in 'chemical clock' reactions?
The short explanation for 'chemical clocks' is that the kinetics of chemical reactions in general are differential equations (the rate at which something reacts tends to depend on its concentration). With a set of competing reaction, you end up with a set of coupled diff. equations, which can often display chaotic behaviour; in the case of the 'chemical clock', you get large periodic oscillations back and forth before equilibrium is reached. Not unsimilar to the http://en.wikipedia.org/wiki/Lorenz_attractor" of Chaos theory.
But entropy-wise I don't see that there's anything particularly distinctive going on.