The ACS salary survey is a poll of ACS members, who are not average chemists and who seem to have higher salaries than most. For example, new PhDs normally enter as something equivalent to Salary.com's "Chemist IV" at the companies I have worked at, starting at the bottom/middle of this distribution and working their way up.
That's a full $10k less than what ACS is reporting as the typical salary for PhDs with 5-14 years since their BS, which is pretty much the same group of people. I think you are better off looking at salary.com's distributions for Chemist IV (younger PhD) and Chemist V (after your first major promotion, small group leader) than the ACS survey.I've posted the two of them against each other above, so that you can see the difference.
I think Chad's comment is correct, in that we do not have an ACS-independent sense of "the average chemist." Also, because larger companies tend to support ACS and to pay employee dues, one suspects that more large company employees are represented than not, driving the salaries up. Finally, there's the methodological issue: ACS Salary Survey numbers are self-reported (you'd be likelier to report if you felt better about your numbers), while Salary.com's numbers are from HR professionals (a different problem: they might be tempted to fluff up their numbers a bit.)
Readers, your thoughts?
UPDATE: Chad has more thoughts on this on his blog.