Whincup's weekend had been on an upward trajectory until the 200km finale, finishing eighth and fifth in the Saturday sprints before qualifying fourth for Sunday's Race 20.
Running as high as third early in the going, Whincup soon had to let team-mate Craig Lowndes through due to a lack of pace in car #1, eventually coming home a distant eighth.
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While a wheel gun malfunction at the second stop contributed to the poor result, Whincup acknowledged that his side of the garage had made a clear step backwards on set-up and was never truly in the fight.
“I was a sitting duck, you can't win races with no pace,” Whincup told Speedcafe.com.
“It was definitely disappointing. We were good on the soft (tyre on Saturday) and had made a gain on the hard in qualifying.
“We should have went away from the weekend with a good feeling, but unfortunately it's left a sour taste because of that last race.”
Dutton explained that the team's current quest to make up ground against pace-setters Prodrive means it has to make bold choices that won't always pay off.
“We over-stepped the mark trying to short-cut the learning process,” Dutton told Speedcafe.com.
“You can take a small step and be close to right but maybe not learn enough, or you can take a big one and then if you take it too far sometimes you can learn nothing. It's a balancing act.”
Lowndes' string of three podiums – and his 25 second advantage over Whincup by the end of Sunday's race – emphasised the level of disparity between set-ups on the two Red Bull entries.
Dutton says that the differing set-up directions at Ipswich were dictated by driver preference, but the aim is always to eventually benefit both cars once all the data and feedback is taken into consideration.
“We did a bit of divide and conquer in terms of testing and development,” he said of the weekend as a whole.
“We don't want to do that but we're really trying to short-cut the deficit.
“The path that #888 went down provided more return on investment. They were doing some really good things.
“There were some positive signs on car #1, but we didn't maximise it and over-stepped the mark a little bit.”
Red Bull's struggles this year have come as a surprise to many considering the relative stability the six-time championship winning team had enjoyed over the off-season.
Some have pointed to the aerodynamic tweak to the Holden as a potential reason for this year's inconsistency, with an unintended balance shift arising from the push to reduce drag from the car.
Dutton, however, stresses that the team is simply having to experiment more this year in order to catch Prodrive, which has streaked away with its formidable FG X Falcon.
“It (the set-up window for the cars) has moved and maybe part of it is the aero, but that's not enough to make the difference at a track like this (Ipswich),” he said.
“To be fair, if this was a test day and they (Prodrive) weren't here we'd think we're on top of the game. The only reason we're not is because they're doing it better.
“Clearly from Townsville to here we closed the gap, that's undeniable, but there's still more work to be done.
“When you're constantly resetting and trying down different paths and they're just working within a good zone fine tuning, the chances are they'll be up the road.”