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.


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