To enable you to use all capabilities of the IR Receiver of your Mac, Remote Buddy is using its own driver. In contrast, all other applications with integrated Apple Remote support usually use the OS X Apple Remote subsystem.
As long as you're running Remote Buddy, Remote Buddy and its driver are responsible for turning the received button presses into actions. As soon as you quit Remote Buddy, this task is again handled by the OS X Apple Remote subsystem.
If other applications don't use the interface to the OS X Apple Remote subsystem correctly, this can lead to the effect that nothing happens when you press a button on your Apple Remote. For as long as you're running Remote Buddy, issues like this are covered by Remote Buddy and it's driver and are therefore not visible to you. However, as soon as you quit Remote Buddy, the OS X Apple Remote subsystem is back in control and any issues caused in it by other applications become visible.
Therefore Remote Buddy is neither the cause of the issue nor is it responsible for it. Instead, the cause of the issue exists independently of Remote Buddy. It's located elsewhere and can also only be solved there.
Although our products can't cause any such issues, we're regularly contacted about such issues and asked for help. In order to make locating and fixing the cause of such issues as easy and efficient as possible, we've developed a free diagnostics tool: Remote Control Diagnostics. It can locate issues with a single click and will provide you with information about the issue as well as with instructions on how you can fix it.