When i look the definition of X-dynaTrace-Application header :
X-dynaTrace-Application: A proxyable Agent, like Apache or NGINX, adds this header. Contains the ID of the RUM application.
if the header contains only the ID of the RUM application.
Why this header longer than 1000 characters ?
I think it should not be that long. As I remember this was discussed on community, and result was that there was fix for agent. But I'm not sure if I remember it correctly 🙂 If this is still issue for you, you should rise support ticket.