Megatowers are tricky, I've had the "overworked/no jobs" situation a couple of times. The thing to remember with megatowers is that they are very slow to react to changes. Those overworked Sims are pretty stupid and can take a couple of Sim months to realize they haven't been called in to work in 7 weeks. Also, if the levels are different wealth, it is quite possible that your low wealth sims are overworked but your medium wealth sims have no jobs. Make sure you're checking the population grid and matching your needs to it. Sims will stay happy if you have at least half of the jobs filled for their wealth class.
Honestly, if you have enough cash, I would demolish both levels and leave the base there for a couple of Sim days (a base without any levels doesn't cost anything, so you don't have to demolish and rebuild the whole tower). Then analyze what your city really needs. If you can't afford to do that, then "trust" the newest level's message, if they are both the same wealth.
Every single time I've had this happen it's been because of traffic problems. Either traffic is so congested at the entrance that the Sims trying to move in are stuck in regional traffic, or they move in but can't get out to the available jobs.
Some general things about megatowers can help as well. Don't mix wealth levels in the same megatower. Make sure the land value around the megatower matches the land value of the sims. Plop parks of appropriate wealth level all around the megatower. If shoppers can't get to their commercial shops they will go to parks and you can keep them happy there.
A good balance for all cities is 3:1:1 Sims:Commercial:Industrial. Learn to read the messages differently, too. If Sims are overworked, read it as "too many jobs" instead of "too few Sims". I usually try converting commercial into residential in bits and pieces until it evens out.
If you have tons of jobs available, but no one seems to be commuting, you may have your commercial too far from the residential. Try interspersing commercial in residential areas, including around the megatowers. Watch your traffic; megatowers dump a lot of people in at once. Low wealth and Medium wealth will use transportation like buses, but High wealth will always drive. They're too good for the bus! 
Place parks and appropriate wealth level commercial near the entrances to get as many as possible to walk.
Also - and forgive if you knew this, but it took me a while to figure it out - Megatowers have 3 entrances. Make sure you have roads connected to all the entrances, to help with traffic flow.
I hope this helps a bit.