Hi,
The thing to understand is that downloading a file directly by an http request (ie probably what your other apps are doing) is going to be much more efficient than the way files are downloaded from the Shared Files feature which is designed to protect the files. So the files are stored on disk with a .config extension which is not allowed to be downloaded by an http request. If the user is in an allowed role then we are opening a filestream to the file and copying it to the response stream of the web request.
If the files don't need protection it would be better to not use the Shared Files feature but just upload them directly to disk and link to them ie from the wysiwyg editor using the link toolbar item you can upload files and link to files.
If the problem is caused by a request timeout on the server you could potentially set a long executionTimeout on the httpruntime element in Web.config
In the latest code we have a config setting you can use without setting it longer globally on the httpruntime element. I'm not sure this change was before the 2.3.8.5 release so it may not work unless you have a recent build from source code or after the coming release of mojoPortal so you may need to use the httpruntime setting for now.
<add key="DownloadScriptTimeout" value="-1" />
-1 means it will use whatever is configured by the httpRuntime element in Web.config, a higher value will be set explicitly as the request timeout on download requests in Shared Files.
Hope that helps,
Joe