runas needs its main input parameter encapsulated in double quotes. The kicker is that cmd.exe does too, if you are passing it a command string with spaces, so you will have to use escape characters for it to work on the windows command prompt:
runas /profile /user:Administrator "cmd.exe /C \"certutil -addstore ROOT E:\\WORK\\UI\\DesktopRecorder\\userdata\\certgen\\X509CA\\ca\\new_ca.crt\""
You would then have to escape that entire string again for it to work in your java code:
String cmd = "runas /profile /user:Administrator \"cmd.exe /C \\\"certutil -addstore ROOT E:\\\\WORK\\\\UI\\\\DesktopRecorder\\\\userdata\\\\certgen\\\\X509CA\\\\ca\\\\new_ca.crt\\\"\"";
Sometimes in runas with a nested cmd call, you don't have to escape the backslash \ characters, so if that fails, you may want to try replacing the sequences of four backslashes with two. Good luck!