Using Jenkins build master on SUSE SLES 12 together with a node machine (Windows Server 2016) connected by JNLP and running under Windows Service as follows:

C:\Program Files (x86)\Java\jre1.8.0_171\bin\java.exe -Xrs -jar agent.jar -jnlpUrl https://jenkins.****.com/computer/windows-node/slave-agent.jnlp -secret **** -workDir "D:\jenkins\windows"

System Information for Slave shows correct information for file.separator:

Windows slave, version 3.19

System Properties

When I execute distributed build on Windows Server for checking out Harvest CA, file.separator used as '/'

Also when I run the following script through pipeline on Windows node, I get file.separator value as '/' (without quote):
echo File.separator if(isUnix()){
echo 'isUnix()'
}else{
echo 'WINDOWS'
}