I'm declaring jfreon & gates r my heroes.
I've been having a similar problem recently using a Samsung Intercept on Virgin Mobile. There was some system conversion within the last month where I was affected. I started to receive an error message that a message could not be sent as the area code was omitted or I used an invalid short. My wife and a friend are the two people I text the most and I could not get the area code to stick for those contacts, so I had to enter the 10 digit number manually. (They are also using Virgin Mobile but apparently have not yet been affected by the system conversion.) That was especially annoying if I needed to respond to their response as the area code still did not "stick" when they would respond.
I tried the editing of another contact where I did not have the problem and that did not fix it (worth a shot).
Clearing the Dialer and Dialer storage got me half way there. After that, when I then tried to create a new text message from the Contacts list on my phone it was filling in a different contact's information. So I then also turned off sync contacts in the contacts settings, edited how the telephone numbers appeared in my stored online Google contacts (I was removing dashes rather than parentheses, but otherwise same premise as gates_r mentioned), and then turned the sync back on. Now, finally, when I click on the Contacts button to text my wife or friend (or use a direct message shortcut), the area code is included. Hooray! I'm now as well off as I was a month ago. Thanks for the new system, Virgin.