We are not aware of any incompatibility of WinBatch with Cisco Prime. Could you please provide further information?
Are you maybe referring to the WinActivate or SendkeysTo function having problems where this app is running in the foreground? If so, have you tried using IntControl 61. It can modify window activations are handled by your script. This IntControl lets you change the current method being used. Some methods may work with some particular windows and not others, so you may need to experiment.
As for WebBatch. It is a CGI scripting language for Web Servers. Where window activations simply do not apply.