I must admit I have not used my mega hoop for a long time but I recall doing my design on the computer. If you have software load the three designs into customizer on your computer in the correct order - as they would stitch out on the machine. Select the hoop in preferences 360 x 150 Mega single. Line up the embroideries in the hoop and enlarge the screen so you can make sure you have no gaps, when you are happy with it, combine the three designs and hey presto you have one stitch out it is no longer partitioned, if I am remembering correctly. When I first got my designer 1 back in 2000 having trouble with the large hoop - cant remember exactly what the problem was now and when I spoke to husqvarna they told me I did not have to select the multi part hoop that was for older software or machines or something. And don't worry we have all hit the wall cause we forgot to leave enough room for the hoop at the back of the machine or bumped it. I even did it with my new Ruby when I used it recently with the 360 x 200 managed to save it just in time! It's worth a try!
When I had that type of problem it was because I didn't get the hoop properly "clicked" into the new position. I was off, so the design was off. Also I have found that as mops said, if the hoop bumps something that can cause the machine to realign it. Also if it is not playing nicely underneath, those stray threads can catch and pull things out of alignment. Machines are so picky :)
I only once had that problem with my Designer1, but it turned out I had placed the machine too close to the wall so when the hoop was moved to postion 3 it hit the wall and thatcaused the trouble. With my Diamond I also have to make sure it is place far enough from the wall and I don't bump into it when it is embroidering at the top of the frame as it sticks out so much.
No idea what else could have caused yours not to line up properly.