java.util.prefs.WindowsPreferences WARNING: Could not open/create prefs root node Software\JavaSoft\Prefsat root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.

This error is because java.util.prefs.WindowsPreferences is trying to save information in HKEY_LOCAL_MACHINE\Software\JavaSoft\Prefs instead of under HKEY_CURRENT_USER\Software\JavaSoft\Prefs.

Open JMeter.bat file as the administrator and so it creates the key HKEY_LOCAL_MACHINE\Software\JavaSoft\Prefs. Hope this resolves the issue.