I used an old 336 first cutting this year for about 1250 bales. It only missed about 20 knots, but they were always on one side and always when under the load of a heavy windrow. I wondered, when I read your post, if perhaps the difference between manually throwing hay into the baler and driving the tractor is simply the rate at which the hay feeds into the machine--much heavier when driving along picking up a fat windrow, thus the bum knotter shows only then?
Which then makes me wonder if it is either some worn knotter parts on that side that can't handle the heavy work load, or else a dull knife at the edges of the plunger that puts a bind on the whole machine and makes the knotter malfunction when plunging a heavier load than when throwing in armloads of hay?
There was a strange accordion affect in the bales from the 336 I used. Now that I'm feeding those bales, often I am unable to easily pick up flecks of hay out of a bale to go and feed them. The hay wasn't cut well, so if, for example, I cut open a bale, then try to grab a third of it and walk off, the hay is still connected to the remaining hay in the bale and doesn't want to pull loose. It is a pain when feeding, but I wondered if it was related to dull knives and that in turn was related to my one knotter side issue?
There are other guys on the forum here with much better engineering minds than mind, so I will look forward to their thoughts on this.