Spotlight does not complete indexing

Question

About 2 months ago I noticed two unusual things on my wife's MBP (see specs below). The first was that the spotlight kept indexing and it did not end regardless of how much time I allowed it to run. On the other hand, time machine backups would start when the external Time Machine HD was connected but it would stall before completing the backup to the point that I would have to cancel the backup completely.  I noticed these two conditions basically at the same time, and at first I thought they were unrelated.
Regarding the spotlight indexing I tried several remedies I found on different forums, but none worked for my particular problem.
Tried several times to rebuild the index by adding and then removing the Macintosh HD into System Preferences/Spotight/Privacy/ panel.
Repaired disk using the [Disk Utility on] install disk.  No problems were found.  Also repaired permissions just in case, but no luck either.
Tried resetting the PRAM.
Tried resetting the home folder permissions and ACLs via reset password utility on the OSX Install disk.
Tried to index the HD from another user account (which had also Administrator privileges).
Using the Console and the Activity Monitor I noticed that when the indexing started, I would see the mds, mdworker and mdworker32 processes running.   Also I would see disk activity and if I clicked on the spotlight icon I would see that the time remaining to complete the index would decrease.  However, at some point both mdworker processes would halt (disappear from the activity monitor), and then the mds process CPU usage would jump to 98% or more.  At this point the spotlight indexing time remaining would start to rise gradually.  I remember seeing indexing completion times as high as 52 hours.  The only way to get out of this was to exclude the Macintosh HD from the spotlight and then reboot the machine.  I am aware that this would also delete whatever progress was made with the index file and that future attempts would need to rebuild the index from scratch.
After making several attempts to rebuild the index and having the same result, I though that there was a maybe corrupted file or folder that would be causing the problem.
In an attempt to isolate the problem, I made the following:
First I had the Macintosh HD excluded from the spotlight search and rebooted the machine.
I added all the folders under Macintosh HD (e.g. Applications, Library, System, Users, etc.). After adding the folders, I then removed Macintosh HD.  This would have the same effect as adding the Macintosh HD excluded, but with the flexibility of being able to build the index by adding folders one by one until the problem showed up again.
I started removing folders from the Spotlight privacy panel until the problem arose.  I noticed the problem had occured when the mds process would reach 98% or more AND the mdworker processes had disappeared from the Activity Monitor.
Once I found the folder where the problem was (in my case was the Users folder), then I would add all the folders under the Users folder and repeat the process again.
After several iterations, I found that the folder causing the problem was ~/Library/Application Support/Mobile Sync/Backup/<UDID>; where <UDID> corresponds the my wife's iPhone's UDID number as seen on iTunes.  By excluding the <UDID> folder the spotlight would run without problems.  If I added this folder, then the problem would reappear.
Turns out that the folders that is causing the problem is the backup folder for my wife’s iPhone.  I don’t mind this folder being indexed, however I also discovered that the Time Machine problem I mentioned earlier would be resolved by excluding this same folder from the TM backups; and THIS concerns me.
I though the problem was a corrupt backup folder so in an attempt to solve this I deleted the backup from iTunes and made a full phone backup.  Unfortunately this did not solve my problem.  I am still not able to include the iPhone backup folder as part of either spotlight or TM.
Any help on this matter is greatly appreciated.
MacBook Pro 13in. Core 2 Duo 2.4GHz (mid 2010)
4GB RAM
OSX 10.6.8
iTunes 11.4
iPhone 5 (model MD641LL/A), iOS 6.1.4

Answer 1

Hello,
I'm seeing the same kind of problem. Here are the symptoms:
-Some or all data from a Mac previously running 10.3, is migrated to a Mac using 10.4. The Migration Assistant is used.
-Spotlight will continuously re-index, stop for a brief period, and repeat, either by itself, or when a search is attempted.
-Erasing the indices with mdutil -E, running fsck, fixing permissions and stopping/starting Spotlight doesn't resolve the problem.
-Excluding the migrated user directory will stop the madness. I.e., other users and shared directories like Applications, are searchable, and Spotlight will stop the continuous re-indexing.
-Recreating the user directory from scratch, and then copying in data from a backup, may once again start the madness.
The big question is, what, exactly, causes the indexing cycle?
The client affected by the problem is very disappointed, and had cause to wonder "how is this any better than Vista? I would have been better off with a Windows PC". I really need to resolve this, but I'm not sure of the best way to get Apple Tech involved with this bug.
Many Macs   Mac OS X (10.4.8)