There is nothing wrong with the server installer. There are two ways to install Typemock on the server: manually or automatically (auto-deploy).
In both ways the -deploy command is needed.
So in your case, I would recommend you to use the following command:
$TYPEMOCK_RUNNER -deploy \"C:\\Program Files\\(x86)\\Typemock\\Isolator\\8.6\\BuildScripts\\AutoDeploy $dotCoverFullPathExe analyze $CCConfigurationFileFullPath /Output=\\\\\\\"$CCRelativeOutputPath\\\\\\\" /TempDir=\\\\\\\"$CCRelativeTempPath\\\\\\\" /TargetWorkingDir=\\\\\\\"$ CCRelativeTargetWorkingDir\\\\\\\" /TargetExecutable=\\\\\\\"$CCNUnitExeFullPath\\\\\\\"
Please keep me updated.