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I would strongly suggest NOT using Excel to save your data. Pick a method to save your data (examples include a simple binary file, TDMS, CSV files, databases, etc.) and if you want to see the data in Excel, export a copy of the data to a format that Excel understands. That way, your data will not be dependent on what the user does.

The RGT uses ActiveX, not .NET. There's a thread with Excel examples here, and I assume at least some of the newer ones are probably with the .NET API - http://forums.ni.com/t5/BreakPoint/Excel-Board/m-p/379682#M2391 Looking at your OP, I see that you're using the RGT. It has a VI which returns the Excel ActiveX references. You should be able to use that to get the Application reference and set it to hidden (I think there's a Visible property, but I didn't really play much with it, so I don't remember for sure that I even did this).

If you open up one of the Excel Report Toolkit VIs, you'll see the .NET functions being used.

Check the Excel .NET API reference from Microsoft. The application object has an option to start hidden.

I just upgraded the LAVA server, so the response should be even better than the already pretty fast previous server. Enjoy.