I've seen something similar occur when 1 user tried to open 2 or more applications from the AccessPoint in rapid succession. I think it occurs because the server does not have time to catch the previous request before a new one is sent. If a user impatiently clicks the same link twice, I suppose this error would come up too. However, I've never seen it happen consistently on 1 server.
Are these Terminal Servers also your QlikView servers? If so, are you clustering them? In general, what is the configuration?
I guess to find out what the problem is, you have to have a look @ your config.xml and your opendoc.js .
Did you use a tunnel? Than you have to set some configuration in <AddQvs>- Tag like: