The badKey errors imply you are using an Agentry.ini that is from a previous version instead of what comes with WM 6.1.
All those badKey messages are informational. The real problem is this one.
11/15/2014 10:48:49, 1, 20, 28, Thr 9712, Error starting Java System Connection Java Back End: java.lang.ClassNotFoundException: com.syclo.sap.workmanager.Server not found from bundle [com.sap.mobile.platform.server.agentry.core]
This message is telling you it couldn't load the java backend hence the No Backends loaded error message you are getting.
I would look at redeploying WM 6.1 again from the SAPWorkMgr611Deployment.exe.
Also are you trying to deploy Development or Production mode Work Manager?
--Bill