There seems to be problems with the method Kernel#system.
For example, when running this in ruby the user is prompted for a password for the Administrator user in the console, before opening a new command prompt:
system("runas /user:Administrator cmd")
Jruby prints the password prompt but does not wait for any input.

Another example:
system("set /p pathName=Enter Input:")
For this Jruby waits for input, but the entered text is not shown until enter is pressed. Then a second press on enter is required to continue.

I've tried this on Windows 8 with JRuby 1.7.16.1