my Jenkins managed part is as follow:
Home Directory: c:\Jenkins
Workspace RootDirectory: d:/JenkinsWorkspace/${ITEM_FULL_NAME}
Build Record Root Directory: ${ITEM_ROOTDIR}/builds
Assuming the above:
Your jobs info should be locate into C:/Jenkins/jobs
The system no matter what should them from this emplacement, make sure this folder is accessible by both user. This is THE folder with the jobs configuration and settings. It also contain the jobs results. I successfully exported those and restore them into another Jenkins.
You may want to check the log just to make sure that nothing went wrong with plugin version, etc...
jenkins.err.log
jenkins.out.log
I always use the service, I changed the user of the service. So I always use the jenkins.xml to start the wars, your args seem to be right, the only thing I see into the file that may change something is the env setting:
<env name="JENKINS_HOME" value="%BASE%"/>
My guess is that you need to do the equivalent into your batch file. maybe make sure the env is set properly. Try to print both user environment to see the difference. But make sure to set this variables into the environment before launching:
set JENKINS_HOME="c:\Jenkins"
"C:\Program Files\Java\jre1.8.0_102\bin\java" -Xmx3048m -mx1024m -jar ${JENKINS_HOME}\jenkins.war
Not sure it will change anythiong but worth the try.