After being fastest throughout free practice, Dani Pedrosa's Brno qualifying hopes suffered a blow when he slid from his Repsol Honda early in Saturday's hour-long session.
And while Yamaha's title leader Jorge Lorenzo went on to set a new pole record, Pedrosa was forced to switch to his spare bike - and unable to match even his free practice best.
The only good news for Pedrosa was that he salvaged a front row start, in third, on his very final lap.
“I had a small crash at the beginning of the session and unfortunately we were unable to use that bike anymore and had to switch to the second bike,” confirmed Pedrosa, whos best lap time was 0.528s from Lorenzo.
“Normally the bikes are very similar and I don't know why, but this time the second bike was much more rigid and I had more chatter, especially in the front.
“We tried to fix it but we weren't able to so in the end I tried to get my best out of it and finally on the last lap I was able to take a front row spot, which is always important.
“Anyway the bike is working well, I just hope tomorrow we can use our preferred bike, as this morning it felt very good, and have a good race.”
Pedrosa, winner last Sunday at Indianapolis, starts Sunday's race 18 points behind Lorenzo.
Team-mate and reigning world champion Casey Stoner, who announced on Thursday he will undergo surgery on his injured ankle in Australia, left Europe from Geneva today with his family as planned.