Disk Utility no longer restores to smaller partitions

Up until today, I've been using Disk Utility to clone my Macbook Pro HD to an external HD. The MBP drive is 750GB, with about 300GB in use. The external 1TB drive has two equally sized partitions of ~500GB. I alternate between the two partitions each time I make a back up. I've been doing this regularly for many years now, and it's saved me on a couple of occasions. My last clone was made on June 2nd. However, today I got this message when trying to make a clone:
Restore Failure
Not enough space on /dev/disk1s4 to restore
This is the first time I've ever had this message pop up. I even tried repartitioning and reformatting the external drive, but it didn't help. The only way I can successfully clone my drive now is by making the external drive one large partition, which results in "Copying blocks. Estimated time: 8 hours". Previously, it took slightly less than 3 hours to clone my drive.
Was there a recent update that changed something with Disk Utility? Is anyone else having this problem?

I seem to remember reading somewhere that Disk Utility will only restore to a smaller partition if you un-select the "Erase destination" check-box. This option does not seem to exist any more in the latest version of Disk Utility (13 (450)). Have you updated to Mountain Lion recently?
A better approach may be to use Time Machine with your external HD. This works nicely with USB disks. You don't need to buy the TimeCapsule hardware. I assume the reason you alternate backups between two partitions is in case it fails during one of the backups. That is less of an issue with Time Machine as it does incremental backups. However, if you want multiple backup disks, Time Machine will automatically alternate backups between them. You can even do the same thing with two partitions on the same disk, but it is safer to use two separate disks in case of a complete disk failure.

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