Make sure you login as sysadmin. Also make sure there is a user created say MDL user which is a member of designer,MWS,Sys admin & webMethods system. This is help on advantage site if you search, i ran into the same issue few weeks back & got it resolved by querying into advantage site.
The Designer log is “/.metadata/.log". It’s relative to the workspace, so each workspace will contain it’s own metadata store and log files. Also, each workspace contains its own metadata for webMethods plugins and configuration.
Sometimes, using a new workspace may resolve any issues you may face in Designer (assuming it’s a problem with the plugins). Of course, this would imply that you would have to configure the new workspace.