Have you set both of your PTO levers correctly? You should see two levers with yellow handles on the right side of your seat.
The lower lever (closer to the floor mat) is the "Mid-PTO lever." This has two positions. Up engages Mid-PTO, and down disengages it. Push it down (the "off" position) to disengage the Mid-PTO.
The upper lever, near the back of the seat close to the seatbelt, has one of two names. It is either called the "PTO gear shift lever" if you do not have independent PTO, or the "PTO clutch control lever" if you do have independent PTO. This lever has two positions and controls basic PTO operation (both rear and mid-). Forward position is "on" and rear position is "off." Note: this lever must be in the "off" position to start the tractor because of a safety switch. Make sure this lever is in the off position, then start the tractor. After the tractor is running, depress the foot clutch (just to be safe, since I don't know if you have independent PTO or not) and move the PTO gear shift lever to the forward position ("on"). Release the foot clutch with the tractor transmission still in neutral. You should now see your rear PTO spinning and it should be fully engaged.
I don't fully understand your situation though. I don't think you can operate the Mid-PTO without also operating the rear PTO. But you can operate the rear PTO without operating the Mid-PTO (if the Mid-PTO lever is in the off position). If the Mid-PTO is engaged, which you say it is, the rear PTO should also be engaged. At least that's what my Kubota operator's manual indicates and I'm going to believe it until I discover otherwise. So maybe you have your PTO levers set between their proper detent positions?
Let me know if this helps.