If you're on OS X 10.6.2: this OS release contains a new HID descriptor for the Apple Remote, that EyeTV currently doesn't support. It will therefore not understand commands issued through the Remote Buddy Virtual Remote. You can put Remote Buddy's Virtual Remote into a "Leopard Compatibility Mode", so it provides the old HID descriptor of OS releases prior to OS 10.6.2 to applications.

This mode currently can't be enabled directly in Remote Buddy, but only through the Candelair preferences pane available at: 
http://www.iospirit.com/labs/candelair/

Alternatively, you could also use Remote Buddy's built-in EyeTV support and use the default mapping for EyeTV.

Best regards, 
Felix Schwarz