Taking a guess but suspect the knives are hitting on the first and second discs. When you have two discs turning the same direction next to each other the timing is more critical to keep the knives from hitting each other. You can not turn the first disc to judge timing, since unlike a discbine, the first disc is being driven by the drive module next to the first disc instead of a drive shaft directly. You must turn the main gearbox so all the backlash is taken up like when the mower is being driven.
Install new knives and pull them straight out. Turn the gearbox and watch when the knives cross closest to each other at the rear of the cutterbar and the front of the cutterbar. You want the gap to be the as close to the same as possible. To change the timing, remove the first disc and the center bolt holding the drive hub to the module. Turn the gearbox so the second disc is pointing straight forward. Remove the first disc hub and turn the hub so the bolt holes in the hub are pointing straight down the cutterbar. There are basically four positions the hub can be installed so the holes point down the cutterbar. Find the set of holes that do this. Before installing a NEW center bolt, put the disc back on and turn the gearbox to check the timing. If still off, then try a different set of hole that line up to the cutter bar..
To check the timing of the rest of the discs, you can use the first disc to turn the cutterbar, just not between the first and second disc.
edit. I need to add to turn the discs in the direction they turn when in operation.