Slow on "Cleaning Up"
I'm also having speed issues with Time Machine. It probably started with OS X 10.7 or 10.8; it seemed as if backing up even a few megabytes (less than 100) could take close to an hour. I thought that it was my drive, but speed tests indicated that the drive was functioning properly. Reformatting didn't help, and neither did changing how the drive was connected to my computer (through an Apple Cinema display vs. directly). It was a nuisance, but it was workable.
Recently I added a second drive to my Time Machine setup. This is done through a built-in feature of OS X, whereby OS X will rotate backups between the drives (backups are made each hour, each drive is used every other hour). This has seemingly wrecked Time Machine. Backups are still sluggish regardless of the drive being used, but I've noticed that it always seems to be "cleaning up." This has resulted in missed backups that can occur for as much as four hours (and possibly longer, but that's the longest that I've observed).
The second drive generally seems to be the one that gets stuck cleaning, but diagnostics indicate that its performance is slightly better than the first drive. Of note, I have Time Machine set to encrypt backups.
At this point I'm going to try working through a few things, from using one drive at a time and seeing if the behaviors change, to decrypting the volumes and seeing if it makes a difference.
I'm posting just to see if anyone has gone through anything similar, and if anyone has any advice for other things to try and check.
