The built-in sensor will never read arbitrary IR remote signals without a ground-up re-implementation of its firmware. It does decoding in firmware and even the driver layer only sees the decoded messages.

The easiest solution to using a universal remote is simply to send Apple IR codes from the universal remote. The machine will simply think you're using an Apple remote - but of course that limits you to 6 buttons. Without using third-party remote apps, other software typically only recognizes those 6 buttons anyway.

Using my receiver, it's technically possible to receive any number of codes in any protocol. However the software I currently sell is geared toward the Apple remote. That's going to change, but I don't know when I'll be shipping additional software yet.

The receiver however *IS* supported by Lirc as an MCE receiver (a number of customers are using it under Linux). So if you can get Lirc up and running you can use any remote codes you want and as many of them as you want.

Back to Boxee... The new software and UI still need a lot of work. I believe they want to stabilize this before they bring it back to the general release platform.