I press any button on the remote a few times and wait about 2-3 minutes and it starts to intermittently accept responses. Then about a minute later everything is perfect. So basically every time I go to use it after a break it takes about 5 minutes to 'wake' up.

It's as if the internal IR receiver is going to sleep and is slow to wake?

I'm using a mid 2011 Mac Mini with the Apple Remote and internal receiver.

Apart from the issue mentioned, this product is fantastic and I'll definitely be buying it if I can get everything working.