I'm getting weird line flicker from line drawings in files after exporting to WMV or even QT (H.264). The static line drawings are originally exported from PowerPoint as jpegs, then animated with overlays in After Effects. Oddly, it only seems to happen in the parts of the file where there are multiple layers. Flicker Removal in Field Options (in Premiere Pro) is a short-term solution as it minimizes, but doesn't completely eliminate the problem. (Frame Blend distorts the image/fonts too much.) Is there a setting to tweak in AME to prevent this? Decoder complexity or keyframe interval? Please, this grasshopper seeks to snatch the pebble from your hand...
Remove Flicker should work, it all depends on the value you set. Before applying it though, you will want to reduce the levels output to 16-235 - pure black and pure white areas are more likely to flicker to due chroma crawl artefacts which happens in areas of high contrast.
So yeah, you get two artefacts compounding the flickering that you see.