It would seem they are trying to sort the bike out for the races rather than for quali of softs, hence why his best laps are aways done on the harder tyres.
As long as that continues he will never get onto the front row & will struggle to get onto row 2.
It is widely acknoweleged that both Stoner & Rossi prefer the hardest tyres available to them, i think lex has mentioned this before that effectively they are both disadvantaged by the now softer construction tyres rather than the ones being used back in 07 & 08, not sure what they were using i 09??