It sounds like your LBS is quoting you the price for the Cross-Check "Virtual Bike" that is listed on Surly's web site, and is different from the "Cross-Check Complete":

Compare this:

http://www.surlybikes.com/virtual_CrossCheck.html (105 components, Cane Creek headset, etc...)

to this:

http://www.surlybikes.com/bikes.html

From their web site:

"What is a virtual bike? It’s a Surly frameset paired with some parts that have been assembled by our U.S. distributor. Aside from our Cross-Check Complete bike, Surly does not actually sell completely built up bikes."

The Cross-Check Complete is still listed on their site with the same build as I paid a bit less than $1k for last year -- a mutt-mix of componentry, including Deore hubs, Tiagra shifters and derailleurs, Ritchey Comp headset, etc...

Since you said the LBS was looking in the distributor catalog, it sounds like they were referencing these "virtual bike" packages, which QBS puts together, rather than the stock Cross-Check that Surly puts together.

Surly's got a dealer locator on their web site, too, if you need to find an LBS that's got their act together a little better.