I used the same approach with my Pioneer C509A plasma - Lintronic box to learn codes, Lintronic software to create XML for Beo5.
What I found was that I needed to manually trim the timings recorded by the Lintronic box, for each button on the Pioneer remote, to ensure that the correct signal length was recorded. To make sure I'd done this properly, I would retest the recorded/saved command by sending it to the TV from the Lintronic box, and double check that it operated the TV.
See page 12 of http://www.lintronic.dk/BEO5.pdf for the procedure.
Once I had the full set of commands double checked in this way, I then created the XML file with the Lintronic software, which works fine with the Beo5.