The two leading rumors are that Amazon wanted the same treatment that Wal-Mart received and the screen scratching returns. While both are plausible, Nintendo had similar problems with Target in the 90's over customer returns, Amazon has bought and sold small amounts of Nintendo hardware from other distributors leading them to come back in stock for small periods of time. This suggests that they have no actual problem selling the devices based on their quality, they just want a deal that they like.
I don't see it getting resolved until Nintendo caves. Amazon is still selling the things that make them money (games and peripherals) while cutting out the things they break even on (or possibly lose a slight amount of money on considering they have to pay shipping costs).