Bruce, what is the issue with the partition table?
Some software (fdisk?) complains about partitions ending halfway across a cylinder, which is quite likely to happen if you dd one drive to another with a different geometry. I don't know exactly why it was considered not a good idea, I'm not even sure if if it's still an issue, but I prefer to create my partitions 'cleanly' with fdisk rather than cloning the layout of a previous drive. There are possibly other reasons why you shouldn't clone drives that way. One you've already found which hadn't thought of is that if you plug the original drive back in at a later time you have multiple partitions with the same UUID, and since Ubuntu relies on UUIDs to recognise partitions this will lead to unpredictable problems. They're supposed to be 'Universally Unique' Identifiers. Having said that, I used to clone drives with dd in the past and it never caused any insurmountable problems...