I have found this problem on the 6000 but only on custom styles and only on those styles on which I have filled up 4 or 5 of the accompaniment parts with busy patterns, eg guitar strums.
I have always presumed I am exceeding the memory capacity (as opposed to the polyphony) of the custom in some way.
Can't say I noticed this on the 5000 which of course had fewer accompaniment parts.
Peter