Check your console log file and look for lines like this (the real log lines will have process IDs and dates):
sandboxd: mdworker deny mach-lookup com.apple.ls.boxd
mdworker: Unable to talk to lsboxd
If you're seeing that, it is probably the source of the problem. Something Appple did with this latest release (also affects Mountain Lion 10.8.2).
I don't know what's really going on other than to say that
mdworker (which scans and indexes files for Spotlight) calls
LSCopyLibraryItemURLs() which eventually sends a message to
lsboxd. The Sandbox policy doesn't allow that, so the worker is killed.
So maybe the policy file is wrong, or maybe
mdworker shouldn't be making that call. I don't know. However, fixing the policy file is relatively easy. POTENTIALLY DANGEROUS, but easy.
Edit these files as root:
Inside the files you'll find the line:
(allow mach-lookup (global-name "com.apple.ocspd"))
Right below it, add the line:
(allow mach-lookup (global-name "com.apple.ls.boxd"))
If you want extra comfort, maybe reboot. Maybe erase your spotlight index and start over:
sudo mdutil -E /
In fact, I still see
mdworker: Unable to talk to lsboxd in my log files but at least now the indexing will finish and Time Machine moves quickly again.