OK, I'm sorry guys, all this was pretty much for nothing - the combing in the problematic clip is actually already there in the source video - something must have gone wrong with Puggo's capture for that particular file. The whole issue was, that AE recognized the files as interlaced, so it set "Separate Fields" to "Lower Field First", which resulted in loss of vertical detail and therefore in both the jaggies and the hiding of the combing artifacts- once it was set to progressive, the jaggies disappeared and the combing became visible. I have another capture from Puggo of the same section, which however has badly blown out whites, so I will have to see what can be done.