We use VB .NET for all of our custom agents. Our main job consists of three custom angents and then jfmerge.
1. Sends a transaction to the mainframe for updating the database.
2. FTP a copy of the DAT file to the HQ server.
3. Check a control file to see if the designated printer is to be changed.
4. Creates the print file that is often a dozen or more pages consisting of several MDF files.
Each of the three custom agents reads the complete DAT file, perhaps modifying something and writes it out again for the following step.
I just checked our most heavilly used server and the last print job, printing a total of 7 MDFs took less than 4 seconds. We are using the same version of Central that you are. This is on a Windows 2003 server that is dedicated to Central. It is running on a Xeon CPU running at 3.40 GHz with 2.00 GB of ram.
We originally wrote these agents using VB 6 and they were not very efficient. That, combined with a slower CPU, resulted in jobs like the one above taking 15-20 seconds.