Nicky Hayden reckoned an incident with Alex de Angelis at the end of Estoril qualifying cost him the chance to achieve a better starting position than his eventual ninth.
The American was 1.1s slower than his Ducati team-mate Casey Stoner, who returned after a two-month lay-off due to illness and immediately claimed a front row spot.
Although Hayden did not think that he would have achieved a similar position, he felt his brush with de Angelis' Gresini Honda had definitely affected his result.
"I thought I maybe had the chance to qualify a little bit better but at the start of my last flying lap de Angelis ran into the back of me on the front straightaway," said Hayden, who was taken out of the last race at Misano by de Angelis.
"I mean, I can understand if you bump a guy in the middle of a second gear corner or something but there I was doing 274km/h and they can see on the data where the bike came unstable because you can see the steering go side to side.
"My first instinct was that something had happened to the bike so I shut off the throttle and it ruined my last flying lap. Anyway, we're on the third row and it's going to be a long, hard race tomorrow."
Hayden feels he has made good progress during the Estoril weekend and is optimistic that he can move through the field in the race if he avoids trouble on the first lap.
"We've made a little bit of progress in every session with every run, just slowly chipping away," he said. "We made quite a big change again this afternoon and dropped another eight tenths off the lap time, although obviously some of that was down to using the softer tyre.
"The team has done a good job - we've tried a couple of things we've never tried before and made some progress.
"I know a lot of guys in my group are going about the same speed but if we can take another little step in the morning we'll be okay. Like always it will be important to get a good start and not get boxed in the first turn. We'll see."
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