OK just done a mega test of Handbrake profiles using handbrake 9.4.

Pr1.1 firmware does not handle chapter markers. All of the Handbrake 9.4 Apple profiles still have chapter markers enabled as standard. If you uncheck chapter markers, you will get the same behavior as pr1.0 ie ipod and iphone profiles will work in N900 media player. AppleTV and Regular/Normal will not play.

The Maemo Wiki profile works sweet as it does not have chapter markers checked.

Use Avidemux to remux your files that have chapter markers, and you should be good to go on PR1.1. Avidemux is very fast so highly recommend