Mike,
Always feel free to bug me .. .anytime
This is the normal behavior of Internet Explorer, and there's absolutely nothing you can do about it .. but if you understand what's happening, I don't think you'll be too worried about it..
When you download a file using IE, you normally have 2 choices, Open or Save. If you selection Open, then IE will download the file to your Temporary Internet Files folder, then open it with the default application for the file extension. Now, if you select the same file again, or another file with the same name, IE cannot save a temporary copy of the file in your Temporary Internet Files folder without overwriting the old one, so IE will add [n] to the filename to make it unique, first [1], then [2], etc.
If your users elect to Save the file to their local hard disk somewhere, instead of Open, then IE will not append the [n] and even if you download the same file 10 times, but elect to Save it, IE will ask if you want to overwrite the old file.
As I said, this is the behavior of IE and there's nothing you can do about it,