It is entirely possible that zoomifyer is trying to write to some sort of temporary folder that ASP.NET does not have access to and the StartInfo properties are not handling the identity authentication properly. If that were the case, I could see the app launching a messagebox showing the error which of course you couldn't see in the web page. Zoomifyer may have also written an event to the windows event log.
You could try setting the web site itself in IIS to run under a specific account to test this out.
On a side note, zoomyfier may not be suitable for use in a web environment. For instance, Microsoft Excel as part of Microsoft Office is not suitable in a web environment. It is easy to have those processes get locked up and hang. Do your IIS settings permit launching of exe's?
Hence, all of these controls that interact with Excel files in ASP.NET.
When you contacted the company about support in ASP.NET, what did they say?