This was a problem during Beta Testing and I think they have found the cause. It has something to do with jobs being saved while a cabinet was in the cabinet editor or LDE and this caused the missing bodies. Hopefully this will be fixed soon.
You can take your offending cabinet into the cabinet editor and right click and choose to remove part editor cuts from entire cabinet then return the cabinet to the job and this will fix the cabinet to re-size. This of course will also remove any part editor cuts you may have placed on the cabinet.
This issue with saving has been solved in the new Version 6. However, it the original issue existed in Version 5, but was not relied on until Version 6, that is why it was never noticed the error in the past.
As you resolve these errors with your seed cabinets, you should hopefully never see them again. A cabinet or job created in Version 6 should never have this error happen.