Are road bike saddles more comfortable in the drops? I have a Specialized Ruby and recently bought a the Ruby Expert saddle to get into racing (crits and gran fondos). The saddle is comfortable and pretty much disappears when I'm riding in the drops, but is uncomfortable when I am riding on the hoods, which is most of the time. Is this normal or a just bad fit? 

I rode it yesterday for 30 miles with a medium chamois.
It's not normal. Road bikes are designed for the hoods to be as comfortable/sustainable as possible. 

If your rear is more comfortable when you're in the drops, you should probably try tilting your saddle back a bit.

However... consider the possibility that when you are in the drops:


The discomfort in wrists, neck and back are greater.
Like you said, you spend less time there.


These could reduce your awareness of saddle discomfort.

As with any saddle discomfort, you should pinpoint exactly where you feel pain, and make a change that reduces pressure there.