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More info: if I use my remote to start a DVD rip, then I can successfully control the playback and menus with aMPdroid. If I start the DVD from within aMPdroid (play on HTPC function), then focus is lost.
My phone: HTC Evo 4G running 2.3.3 gingerbread. This may be an HTC thing because they have some sort of memory management bug that appeared after their gingerbread update. Thorsten, what phone/tablet are you using?

Don't know why this was voted down. It's a clear bug.