If you have added an action for the Green Button (MCE Media Center command) under Tools>Options>Remote control>Commands, you have overridden the default behaviour for the Green Button. That is why the Green Button isn't working for you.
You will notice that under Tools>Options>Remote control>Commands there is no pre-defined item in the list for the Green Button. That is because it is basic to MC functionality, in the same way it is basic to WMC functionality. You should not program anything against the Green Button in the remote control commands. You should delete that record, and the Green Button will revert to its default behaviour and start working again. In fact, while I have tried modifying a few of those commands, I have reverted all but one, and added one other, using the extended buttons available through the Logitech remote setup. When people are having trouble with their MCE remote I usually advise them to reset all remote commands back to the default, unless they really know what they are doing. You do not have to train IR Commands for all MC functions. The functions listed under Tools>Options>Remote control>Commands are already linked to default MCE IR commands. You only make changes in that section when you want to change the behaviour of default MCE commands, or add new commands linked to new IR command codes.
Basically, the functionality in MC for IR commands is a bit limited, which is partly why people use EventGhost and other tools to gain additional functionality.
MC sees all MCE IR commands, including the Green Button. But it doesn't see much in the way of other IR commands. Therefore, there aren't many "spare IR commands" that you can associated other functions to. However, if you look under Tools>Options>Remote control>Devices & Options, you will see that you can pick other devices that MC can respond to. You should have both "Microsoft MCE" and "Remote, keyboard, gamepad or other HID" selected, and both should be active, and that will give you some more choices.
For example, if your Gyration remote control can send keyboard commands, then the "Remote, keyboard, gamepad or other HID" MC device will be able to detect those commands. In my case that has been of limited use, as my Logitech only supports keyboard commands that are mostly already used by Windows, so if I use them for MC I lose the default Windows functionality.
There may be others who can provide better advice, but I think you need to look to your Gyration remote control setup, if you wish to keep using that remote. I suspect that the answer is there, because quite a few people really love those remotes.