Deflicker in Stop Motion when the usual plugins wont work?

Question

The movie is a stop motion with a coloured background made up out of tiles. (I can't upload it because the client won't be very happy seeing his project online)
Guys walk around flipping the tiles and thus the colour. This way each time a new logo is formed.
At the last minute they decided the scene would be bigger so I bought a new and untested 17-40L canon lens, unfortunately this gave some pretty bad and unregular aprture flicker.
The problem is any plugin I tried, sees the guys walking in and out of the frame as flicker, since they just watch the histogram.
Is there any tool I can use that just lets me pick a point and stabilizes the scene in regard to that one point.
Then I can keyframe it everytime a guy might walk in front of it, or it changes to another colour.
I also tried change to color because the background is always made up out of just two colours, but this either gives me a very noisy result or it affects skin tones with the slightly reddish backgrounds.
All the auto correction functions have too much effect on the overal look of the clip which is very bright and coloured, so no shadow area's and no neutral grays.
The best result I had was with a time blend. This was incredibly smooth in terms of brightness, but ofcours the client will not be happy about the people in the frame being warped over 5-10 frames.
Tried these plugins with horrible results.
http://www.granitebaysoftware.com/Default.aspx
http://www.revisionfx.com/products/denoise/
Thanks, this would trully be a live saver!

Answer 1

Hi,
Thanks for the reply.
We did extensive testing before the shot, since this couldn't be redone. The mistake was buying a new and untested lens relying on Canon and the fame of L lenses.
Next time I have to use this lens I'll put in a grey card which I'll crop out.
The camera was set on manual and raw. The development was focused on reducing small changes by pulling shadows and highlights.
The mishap was the new lens which didn't open and close reliably at F8. Meaning there where small differences in the opening at F8.
Like I explained Color Stabilizer won't work because of the lack of black or midpoints.
Forget all of the above
I just realized I do have a black and grey point.
When I cropped from 2*3 to 16*9, I cropped out a black tripod leg with a grey wheel.
But before I do another export of +10k raws, can you use the color stabilizer on just a black and grey? I do have higlights but they are never in the same place and never get exactly the same lighting.