I see. The loading and displaying of flash is completely handled by Internet Explorer. The Tournament Director can't really do anything to affect that. I suspect there's a caching issue going on, and when the file is local, IE can easily see that the SWF file has been updated (it can read the Date Modified on the file). If it were over VPN, it would be the same situation, since it would be on a connected drive, and again IE could just read the Date Modified. Getting the SWF from a web server is different, using a completely different protocol. With what I know about HTTP protocol, there's no reason it shouldn't be able to just as easily check to see if file has been updated and retrieve it again from the web server if so. In fact, that's all part of the HTTP protocol. But IE may be doing something else ... maybe a shortcut (or a bug) where it doesn't retrieve the SWF file from the server if it has the file already in its cache, regardless of the modified date.
A simple thing to try is clearing IE's cache before and/or after making your change(s).
A more involved, and annoying, solution might be to rename the SWF file when you make a change, and update the layout to point to the new name. That might work around any caching. For example, if you've got an ad on your web server named myad.swf, and referenced in your layout as
http://yourwebserver.com/path/to/myad.swf, you could:
(1) Copy myad.swf to myad1.swf
(2) Make changes to myad1.swf
(3) Modify the layout to point to
http://yourwebserver.com/path/to/myad1.swfRepeat when you need to make changes, using a different filename each time (myad2.swf, myad3.swf, etc).