I had been having problems with Motion introducing violent artifacts into the audio of imported video clips. It still does this but only with clips that have two mono tracks. If these tracks are brought in as 'open as project' or imported into an existing project with the default 'mix to stereo', they get distorted. However, if they are imported as 'import all tracks' (mix to stereo' unchecked) they are perfectly normal.
None of these clips has ever been a problem in FCP6 and there is a way to get them into Motion 5 but it seems like a bug that mix to stereo can't deal with them.
Mac Pro 6-core 3.33-12Gb, iMac 24" 3.06 Core Duo 8Gb, MacBook Pro 13" 2.7 Core i7 8Gb