There should never be a difference in "time to do flatwork" and "time to jump". When you have an issue like yours it is almost always from 1) weak foundation of flatwork, 2) not riding properly when the jumps come in, or most commonly 3) all of the above (2 caused by 1).
If your horse goes well on the flat but gets thrown off kilter once you throw a jump in there, there's a good chance he isn't going as well on the flat as you think. Not only must he be rhythmical and balanced at the canter, he must also be easily adjustable in pace and length of stride, be able to move laterally, and responsive to all aids. Just to name a few.
If you're absolutely certain your flatwork is just fine, do some stuff on the flat, jump ONE jump, and immediately continue with your flatwork. When your horse is balanced and responsive again, jump another jump. If your horse lands from the first jump strung out and unbalanced, fix him. If you can't? There's a hole in your foundation.