The running rancher-server/agent and their related  containers can be viewed using 
 docker ps. (Remember rancher server/agent etc can run on other linux distros as well as rancheros. ) . eg:
Code:
root@rancher:~# docker ps
CONTAINER ID		IMAGE							 COMMAND				  CREATED			 STATUS			  PORTS							  NAM
ES
3176a6077906		rancher/scheduler:v0.8.2		  "/.r/r /rancher-en..."   3 days ago		  Up About a minute									  r-s
cheduler-scheduler-1-7030b29a
8d23629722d9		rancher/storage-nfs:v0.8.5		"start.sh storage ..."   11 days ago		 Up About a minute									  r-n
fs-nfs-driver-1-00ec47cc
44213a15c28d		rancher/healthcheck:v0.3.3		"/.r/r /rancher-en..."   2 weeks ago		 Up About a minute									  r-h
ealthcheck-healthcheck-1-14795046
74d04ac0295c		rancher/net:v0.13.5			   "/rancher-entrypoi..."   2 weeks ago		 Up About a minute									  r-i
psec-cni-driver-1-b8e46d60
6cd01ac9ac24		rancher/dns:v0.15.3			   "/rancher-entrypoi..."   2 weeks ago		 Up About a minute									  r-n
etwork-services-metadata-dns-1-aede8559
b5381f05f099		rancher/network-manager:v0.7.18   "/rancher-entrypoi..."   2 weeks ago		 Up About a minute									  r-n
etwork-services-network-manager-1-7bcc510f
7fd18fc19e39		rancher/net:holder				"/.r/r /rancher-en..."   2 weeks ago		 Up About a minute									  r-i
psec-ipsec-1-987d5a01
3f60422fbf82		rancher/metadata:v0.9.5		   "/rancher-entrypoi..."   2 weeks ago		 Up About a minute									  r-n
etwork-services-metadata-1-3a5fc1ad
1379cbb07009		rancher/agent:v1.2.7			  "/run.sh run"			2 weeks ago		 Up 3 minutes										   ran
cher-agent
defcfa170620		rancher/server					"/usr/bin/entry /u..."   2 weeks ago		 Up 3 minutes		3306/tcp, 0.0.0.0:8080->8080/tcp   won
derful_varahamihira
 
I believe all the rancher config data is held internally, some of it in SQL tables.  See here for further details: 
http://rancher.com/docs/rancher/v1.6/en/faqs/server/
You've not said if the host you've registered with the rancher-server, and whose details are being lost,  is the same host that's actually running the rancher-server.  Assuming this is true and you only have a single DockerVM running, then I have not encountered your problem in my limited use of rancher while testing in FreeNAS 11.1, nor using the same combination running in virtualbox on a linux desktop.
Other than looking at the references I gave you to troubleshoot your problem, the rancher system logs might provide some clues.  I'm afraid I cannot advise further.