Sue Ellis, an expert in literacy at Strathclyde University, has published a report which highlights variations between the national 5-14 test results for P7 pupils involved in the phonics programme and the psychological test results used to proclaim its success.
Her report, which appears in the December issue of the Journal for Early Childhood Literacy, notes the study's findings: that, after seven years of following the synthetic phonics programme, pupils were three years and six months ahead of their chronological age in decoding words, one year and nine months ahead in spelling, and 3.5 months above the expected level for reading comprehension.
However, national test results for the eight primary schools involved in the phonics study show a variability that does not reflect the poverty levels of pupils.
The results for Level D attainment in P7 in reading in 2003-04 show that three schools, which had free school meal entitlements well above the national average - 56 per cent, 76 per cent and 33 per cent - were attaining national averages and in two cases exceeding them.
But, two other schools with similar catchments, did less well. And the results of the largest school, which serves the most advantaged area and has an FSM entitlement of just 14 per cent, were only in line with national 5-14 results.
"Even 82 per cent attainment in the following year (2004-05) is disappointing. Schools with similar catchments in local authorities such as East Renfrewshire were at this time regularly attaining in the region of 90 per cent plus," writes Ms Ellis.
She suggests these wide variations in school performance could be important for policy-makers, particularly in England, who have been inclined to accept the results from the phonics programme which has a narrower focus than wider test results.
The Clackmannanshire project, devised and evaluated by Rhona Johnston and Joyce Watson of St Andrews University, was a major driver in the Rose Report on literacy in England which persuaded English education ministers to instruct teachers to use synthetic phonics reading methods.
Ms Ellis insists that the national test results should not be seen as a direct challenge to the standardised test results reported for the Clackmannanshire study, as they have emerged from different models and measured different things: "This analysis shows that one cohort's reading achievement can look quite different under different lenses."
She suggests that the real lesson from Clackmannanshire should be that any study driven by only one way of doing things can offer only "limited insights".
West Dunbartonshire's 10-year literacy programme, which used a number of approaches to achieve its aim, was "possibly the most successful intervention" because its starting point was that curriculum change was about contexts and staff as well as programmes and teaching content. "This intervention was not driven by a desire to know which theory works the best, but by the need to address complex, real-world literacy issues," she adds.
Lesley Robertson, Clackmannanshire Council's service manager for continuous improvement and education 3-12, said: "Synthetic phonics is an important aspect in pupils' acquisition of literacy skills, and we are fully committed to pursuing the approach which has been shown to be significant in developing functional literacy in almost all pupils.
"However, more remains to be done to close the gap between the very high level of success for all and the number of pupils who achieve level D at the end of P7.
"There are many skills required to achieve the levels of comprehension expected at levels D and E, but if pupils are not functionally literate, they are unlikely ever to be able to demonstrate more sophisticated higher order reading skills."