Two options:
Option A: Send us a short clip like 5 frames with your AE project to validate your setup is fine. Please note we are on our way to IBC this week so there will be a lag in response.
Option B: In some cases due to the nature of deinterlacing, if you have fine horizontal lines they can sort of appear and disappear per field.
So option B is to use FieldsKit before it
Then the workflow becomes:
Footage: Turn Fields Off
Comp 1: FieldsKit
Comp 2: Twixtor
With FieldsKit you have a mode to deinterlace only where it moves
This should remove flickering
Then you have two options: work at 59.94 (use double FPS Mode in AE) or 29.97
The difference is at 29.97 you will keep only one field per frame and at 59.94 you will generate 2 fields per frame which might be better for fast action on a static background. You will have to set appropriately Twixtor Input: FPS then.
More reading here:
https://www.revisionfx.com/generalfaqsFieldSupport.htm
Pierre