Let me take a shot at explaining the problem. With a 2 stage clutch like you are used to, there is no problem, because as you let out the clutch a little bit the first thing to engage is the PTO, and you can wait for the implement to "spin up" before you let out some more to engage the final drive and make the tractor move. Likewise if you press in on the clutch the tractor can be brought to a smooth stop while the implement mass is still engaged and being driven by the engine. Again no problem and this is a pretty good system. Now, that said, the cheaper tractors, like my old Kubota B7500 and the Kioti CK20S both with standard transmissions never had 2 stage clutches for PTO operation.
They just have transmission driven PTO's with a single stage clutch.. You let out the clutch the tractor begins to move and the PTO implement starts to spin up. Not worth a crap for baling hay, or rotary cutting for that matter. You need to start a rotary cutter raised up a bit so you don't choke it immediately until it gets spun up.
The bigger and heavier the cutter the worse it is. BUT they are supposed to be safe in that as you push the clutch in to change gears or for any reason, the over running clutch built into the PTO drive line does not allow the spinning mass of the implement to drive the rear wheels with power to continue moving the tractor forward even though the engine is disengaged from the driveline by the main single stage clutch being pushed in. The "ratcheting or clicking" sound you hear is the overrunning clutch doing it's job.
The overrunning clutch is supposed to allow power to be transferred from the transmission but NOT back into the transmission from the spinning mass.
Some of the old Fords, from 70 years ago did not have any internal overrunning clutch, and they exhibited the same problem the OP is talking about. The inability to stop the "darn" tractor when the clutch is pushed in and he is standing on the brakes and the tractor is still moving until the energy in the spinning mass is converted to heat by the brake pads.
This is very dangerous, and caused injuries or even fatalities back "in the day".. It ain't supposed to happen in 2014.