The 4000S has the Black Chili compound

Current black 4000 models have the Black Chili but ONLY in the black tires... if you buy colored tires, no chili.

Older 4000 models did not have Black Chili
I am pretty sure that the boxes indicate whether you are getting chili or not...

There are the obvious cosmetic differences too ~ silver lettering as mentioned on the 4000S (but it's not "raised" iirc...)

The 4000S is also only available in like one size.