It is set up on that way the server as well. The connection in the DBC works properly if I create it on site. I simply can't re-create it programmatically.

Here's what GenDBC created from the original DBC:
CREATE CONNECTION CONNECT1 ;
DATASOURCE "MyDataSource" ;
USERID "" ;
PASSWORD ""

Also specified in that connection dialog was a database name which GENDBC didn't use

I'd like to do something more along the lines of:
CREATE CONNECTION CONNECT1 ;
CONNSTRING "DRIVER=SQL Server;
SERVER=MyServer;
NETWORK=DBMSSOCN;
DATABASE=MyDatabase;
Trusted_Connection=Yes"