Unlike previous versions of Twixtor, the Separate Fields feature of After Effects for source material should be set as is appropriate for the footage. (Note that you can also interpret the footage with Separate Fields set to None, which means older projects will work as expected).
If you have 3:2 pulldown in your material, you should remove it first before applying Twixtor (either using AE's pulldown removal feature, or by using our FieldsKit product).
Note that you must also specify the field order setting within Twixtor in addition to how you’ve interpreted the footage with AE's Interpret footage command.
Set AE's Separate Fields setting as is appropriate for the footage:
Interlacing upon output:Simply set the Field Rendering setting of AE's Render Settings appropriately. If set to "Off" Twixtor will produce progressive frame material. If set to Upper Field First or Lower Field First, Twixtor will create interlaced material as appropriate, using the time-interpolation settings specified in the Twixtor plugin. Note that this requirement is different from pre-version 4 versions of Twixtor.
Set AE's Field Render setting as is desired for final output: