Snapmarks are not longer supported and work on them has been put on hold because of the new calibration tool. If you have not performed the calibration I highly suggest that you do.
Do not reposition to make it look like it will line up. The biggest thing when using snapmarks is to make sure you have the thickness set to the thickness of the jig and not what you are engraving. Then set the thickness of what you are engraving in the engraving settings. If the snapmark symbols line up after telling it to snap then you are good to go.