Falling snow affected the track during the qualifying round for many of the top 10 ranked sliders who had to tackle the course first, setting a line for others to follow.
Despite missing the cut for the top 10 shoot-out, Lincoln-Smith is still well placed in the Skeleton World Cup standings, holding down eighth place.
A new event format was used at Winterberg, with two qualifying runs producing a top 10, with the fastest sliders competing in the final on the following day.
However, heavy snowfalls meant that the first of the two runs was cancelled, with the times of the second run alone determining who would make the final.
Lincoln-Smith, an Australian Institute of Sport scholarship holder, was one of the early runners and was one of many top competitors who appeared to be disadvantaged by the conditions.
The run looked to start well when she set very fast times at the opening two check points, however she slowed the further she went, crossing the line in fourth place from her start position of six, only to watch other later sliders move ahead of her. In the end she narrowly missed qualifying for the final by one place, and just 0.05 of a second.
Lincoln-Smith shared her disappointment of missing the final with other fancied runners, including Anja Huber, Melissa Hollingsworth and Shelley Rudman.
"I'm usually the first to admit that I should have done more or better, but I really don't think I could have done any more," Lincoln-Smith said.
"I had the best run I've ever had on this track and felt great on my sled, but with the weather the way it was and the way they do the race draw for the top 10 girls, there really wasn't much I could do.
"I slid my best, and alongside a few of the other top girls, got done over by the weather gods.
"The race should have been canceled. It's done now though and I took a lot of confidence from the race and know when I go back there I can drive that track well, which is something I've always struggled with at Winterberg as it's always being my worst race result and least favourite track to drive."
The event was won by Canadian, Amy Gough, with Germans Katharina Heinz and Marion Thees in second and third place.
The 2011/2012 Skeleton World Cup resumes in Konigssee, Germany, on January 13.