I own a SP-404 and i am mostly using it for recording samples directly from a synth or organ. It has been working fine, however lately my samples has began to sometimes sound like it is peaking or distorted. It is not because the level is to high, as it also occurs when the level of both the amp and the sampler is turned down low. It seems to be happening pretty randomly (every 3th-4th time the sample is played)

Have anyone experienced this, and is there a solution to the problem?

did u mean the audio input level is turned down low?
cos that is what ud need..

maybe, just maybe, its a sign of the flash card dying.. dodgy flash cards sometimes dont playback correctly.. if you record to bank C-J, could u try recording on bank A or B to see if its a card thing?