from what I’m reading, he’s not deinterlacing at all. He says he’s rendering interlaced H.264
That’s probably the problem he’s seeing when it playing back.
The footage is originally DV format? If it’s DV it’s probably gonna be lower field first interlaced.
Make sure the footage is interpreted correctly in After Effects, then either render out to animation (lossless) with no interlacing, then compress using another program, setting input and output to progressive.
Or render out interlaced from after effects, and set a deinterlacer in your compression program.