Using version QuickBooks PRO 2005, I have developed a .Net application that is making use of 5 company QBW files at one time. I have tried using both DSN's (5 different ones) and DSN-less connections  with the same results. I have given the Flexquarters QODBC application access in QuickBooks administrator screen for each QuickBook company file. When the .Net application trieds to connect to any company file I get the following message:

QB Begin Session Failed. Error = 800040418, This application has not accessed this QuickBooks company data file before. The QuickBooks administrator must grant an application permission to access a QuickBooks company data file for the first time.

The DSN's work with Excel fine without having to add it as an authorized application in any QuickBook company file.  Thanks in advance for your help.

Firstly, QuickBooks only supports one company file being open at the one point of time. You will need to open and close connections with a delay between company files.

Applications must also be authorized to use QuickBooks. For example MS Access users must be authorized in QuickBooks, not just QODBC. I suggest you open QuickBooks and open the company file as the QuickBooks Admin user, then open a DSN connection for that company file in your .NET application and grant your application permission to access the QuickBooks company data file.