@ohno, can your analytics split split out only the traffic that has a Google Search referrer? and then allow you to drill down deeper - for keyword, landing page, time and geo-location?
That's the kind of data I'd want to start with. Also connect your sale or conversion data up with traffic source.
From what you describe, you may be getting "dayparted" - good rankings for just some part of the day. You also may be getting a heavy duty geographic filter. But those are only my initial suspicions and it takes some digging to see if either of those are really in play.