At the risk of being anecdotal, I would like to add my own doubts about the implications of the rise at KS2 SATS scores to those of the Durham researchers (TES 100502).
Until recently, I taught at an Independent School whose Juniors' KS2 SATS scores were very high. In September 2001, however, the Year 7 were so weak at writing that we had to put them in ability groupings once a week to give the less able what were, to use a politically incorrect term, 'remedial' lessons in basic literacy.
Over the years, pupils' ability to do a simple comprehension and write a piece of undemanding narrative at the beginning of Year 7 had, if anything, deteriorated slightly, and a major trend seemed to be that a greater proportion of them could no longer read or write independently for any length of time.
During the past six months, I have done supply in a variety of state and independent schools in Eastern England and talked to a good many teachers. My impression is that the majority of them feel that there has been no great change for the better in new Year 7s over the past few years - except in their SATS scores, of course.