I haven't noticed it in a long time, so I presume it was fixed with a firmware update a while back, but there did used to be a fairly nasty bug that would cause the effects section to go nuts and sound really messed up and aliased like you describe - it wouldn't go away unless you power cycled the machine.
Apart from that, I have nothing but good words to say about the effects on the P6 - so much so that if it were released as a standalone effect pedal, I'd buy it in a second to use with my other synths.