I have a simple application that reads a large text file (290,000) lines, and for each line reorganizes the data into a set of objects. These objects are then written to an output file of about 4,000 lines.

General Logic

Get Input File from User
Open File Using FileSystemObject
For Each Line in File
Sort Into Appropriate Objects
Combine Statistical Data
Get Output File from User
Write Each Object/Subobject to OutPut File

My problem arises during the file read. If focus is switched from the application during the read, the application will stop responding. I have reproduced this behavior both in and out of the dev environment. I am assuming that when the application loses focus, the system deprioritizes the process and that causes a problem.

What I'd like is for the application to run like a background application, but allow for user input; I believe this will solve the focus problem. Does anyone know how to configure this? In addition, any other ideas on what is causing this would be helpful.
Both the dev and production environment are Windows XP, Dev is SP3, Production is SP2. References to Microsoft Scripting Runtime and Common Dialog Control.