If you use X and/or Y offsets at layer level or in cutting, it can happen that the generated (rectangle) registration job is not be the best choice, depending on the layer source you use for registration.
It is advised to use the actual image content of a specific layer on the front or back for a registration job.
When you need to cut from the back and flip the cut job, and you also want to define registration, you also need to flip the registration job. In case you need to use step and repeat on such a job or recipe, this will lead to unexpected results when using interleaved offsets.
Use one of the front layers as a registration layer (the actual image content), avoid using interleaved offsets, or use cut path on front instead without flipping.