If you are viewing the search rankings report over a date range of more than a single day, rankings for queries that do not generate many visitors won't always be accurate. This is one of the few reports whose values represent averages rather than sums, but the centralized code used to generate these reports does not currently support averages appropriately.

The problem arises that a given search query does not necessarily occur on every day in a date range, and even if it did, is not guaranteed to have rankings because the visitors may not have come from Google.

The code sums up all the rankings it has and then divides by the number of days in that range to get an average, but for days without rankings, the ranking is "0", which makes the final average considerably lower than it actually is.

Long term, this will be fixed, but it is harder than it sounds. This is just to inform you we are aware of this problem and are considering solutions.