Something is wrong with the contents of the WmRoot package or the server application access to them. Apparently the /packages/WmRoot/manifest.v3 file is correct, because the startup service list of WmRoot is found. Also there are possibly correct and accessible node.ndf files under /packages/WmRoot/ns, because those are the logical equivalent of deployment descriptors that tell IS there is a server/record for the IS namespace and you are not getting “service not found” errors.
Check on your disk under /packages/WmRoot/code/classes for a bunch of .class files. Particularly in /packages/WmRoot/code/classes/wm/server/net/.
Did you install with a different account than the one that is running the IS?
#Integration-Server-and-ESB#webMethods#webMethods-General