Paul,
Have you tried learning the codes? I suspect you will be able to learn single keypresses but combinational keypresses such as Ctrl-A, Shift-A, etc... will present problems.
Also, the mouse may present some problems well.
The IR Scheme for keyboards is pretty complex and cannot always be handled by the pronto. Not that the codes can't be learned, but rather that the sequence in which the keyboard generates codes cannot always be replicated on the pronto.
Please also see this thread.
[Link: remotecentral.com]