I assume that most people don't use the optical out so it hasn't been a big deal.
In my case, one of my Express base stations is connected by optical to my Denon receiver and works great.
Like you, a number of folks actually do "bypass" the base station's internal DAC and feed their analog audio equipment via an external DAC. I haven't seen any wide-spread reports that they were having the same issue as you.
It may be an optical issue, and it may also be DAC specific. I have two different DACs, and the one I normally use was the one not playing nice with the new AE. I tried my other one and it worked fine. My first generation AE did just fine with both of them. Weird. I may try to take it back anyway to see if that makes a difference.