However, engineer Mark Dutton was confident the issue would be resolved - and Whincup bounced back to prove it this morning.
Whincup held off the promising Prodrive Falcons, with Chaz Mostert home second and Championship leader Mark Winterbottom third.
It was an impressive effort by Scott Pye, who came home fifth after leading the session at a time. Plenty of eyes will be on the XBOX coloured DJR Team Penske Falcon this weekend, with Marcos Ambrose back as a co-driver.
"I was really disappointed there, we were up a couple of tenths and I sort of threw it away at the end there... nice to be disappointed with top five," Pye said, getting out of the car.
"Every time we come out we're getting stronger and moving forward. Looking forward to getting Marcos in the car his afternoon."
David Reynolds came home fourth, meaning FG X Falcons held four of the top five positions.
Jack Perkins, in the Holden Racing Team #22 came home 13th, and Craig Lowndes was back in 23rd.