The Keyspan Express wake up feature wakes up the computer regardless 
of which remote you use. That's a hardware limitation of the Keyspan 
Express as that receiver does not do any pattern or remote control 
code recognition at all. That has the benefit that you can use 
virtually any remote with it as long as the software on the computer 
can make sense of it, yet it has this single drawback.

Apple's built-in IR receiver takes the opposite approach: pattern and 
ID recognition in hardware, no wakeup on other remotes, but it 
consequently will never be able to handle anything else than the Apple 
Remotes.

I'll see whether I can include an option to turn the wake-up support 
on and off via the preferences in a future release, but can't promise 
anything.

Best regards, 
Felix Schwarz