Suffering from technical problems throughout the weekend with the JG Speedfit Kawasaki, Hickman still got through to the second stage of qualifying and set his fastest-ever lap around the Hampshire circuit.
But he just missed out on the one-lap Superpole challenge by 0.007secs and started the first race from 10th position.
A dramatic first race saw the Lincolnshire rider mixing it with the front runners and up into fifth place on lap nine.
But the race was red flagged, and the 12-lap re-run was taken from positions on lap eight when Hicky was in eighth place.
At the restart he moved up to sixth on the first lap, but gradually dropped back as his tyre began to disintegrate and he finished the race in 12th place.
“I feel robbed,” he said. “That was my worst-ever result here at Thruxton.
“We were racing on the softer tyre and it just wouldn’t do the 26 laps. Rules meant that we couldn’t change tyres after a red flag so I finished 12th and started the second race from a lowly 13th position.”
As race two got under way a determined Hickman made up ground from the off, and by lap six he had moved from 11th to fifth and was embroiled in a battle for position with Dan Linfoot and his two team-mates, James Ellison and Leon Haslam.
However, he held his ground and crossed the finish line in a very close sixth place to pick up 10 championship points to add to the four from race one.
Unfortunately it was not enough to maintain his ninth position in the rider standings and he dropped a place to 10th on 96 points.
“It has been a really disappointing weekend for the whole team,” he added. “I was probably the strongest of the three during practice, but during the races I just couldn’t seem to catch a break.
“The opening part of that first race was going well and exactly how I thought it would, but with the red flag and the countback it meant by the time I started the re-run my tyre had already done 14 laps and I just wasn’t able to match my earlier pace.
“The second race went better and the bike felt good, but starting from 13th meant I had to use my tyre a little more to get towards the front and just slipped back to sixth on the last lap.
“It’s not great but it’s definitely more where we need to be so I’m happy.”
The next round is at Brands Hatch early next month where Hicky will be hoping for a good weekend with no problems in the run-up to the top six shoot-out.