A lot of riders in our club wear the Sp. S-works, both men and women. That is a first I heard of the problem that you mention. I know Specialized has a shoe fitting system. You might want to check with your LBS. There are a few different inserts that they made depending on the arch of your foot. You would stand on a "pad" best I can explain that gives an outline of your foot.
I wear the Specialized Ember and went up a size from a Specialized Mtn shoe that I had since 2005. The tongue is a bit longer. I don't walk on it much at all so I did not find it to be an issue.
I am not sure if this info helps, but it could be the way your foot sits in the shoe. Just my 2 cents.
2012 Specialized Amira S-Works
2012 Vita Elite
2011 Specialized Dolce Elite (raffle prize) - Riva Road 155
Ralaigh Tara Mtn Bike