A new report is out that suggests a fault may exist in Apple's Time Machine service, causing internal drives to be automatically and silently added to Time Machine's exclusion list, resulting in the service not backing up the data on these drives and not notifying the user of the change.
As outlined on Diglloyd's Mac Performance Guide blog, this problem appears to be situational to setups where many internal drives are being managed. To see this happen, be sure one of your internal drives is mounted and available, and then add it to the Time Machine exclusion list and restart your computer. After the system boots, reopen the Time Machine exclusion list and then unmount the drive you previously excluded.
When performing these steps, those experiencing this issue will see the drive disappear from the exclusion list as expected but then be replaced by another mounted drive in the system that is subsequently excluded from backups. This unintended addition to the exclusion list will result in this new drive's data not being backed up.
It is important to not confuse this behavior with Time Machine's default behavior for handing external USB and FireWire drives. Time Machine is built to exclude external drives by default, so only the Mac's internal drives are backed up and not every USB thumbdrive you use is copied to your backups.
If indeed a bug, this issue appears to only be a problem for those with rather elaborate drive setups, with heavily partitioned multiple internal drives. In most cases Mac users have one or perhaps two internal drives on their systems that are handled by Time Machine quite well.
Additionally, this bug may be more specific to individual setups instead of being a problem experienced by all Mac users. While some readers have confirmed seeing the problem that Diglloyd outlined, others with similar setups have not seen this specific problem. Though Diglloyd claims it has been around since OS X Lion, this inconsistency makes it difficult to find a single cause of the problem. However, one possibility may lie in how Time Machine identifies drives to include or exclude.
When handling individual files and folders Time Machine will exclude by file path; however, when managing volumes it does so by using their UUIDs, which may be the source of the problem for those experiencing this bug. The UUID for a volume ought to be a unique number that is generated when it is formatted, and is based on the drive's properties, but if for some reason the UUID is blank (all zeros) or otherwise matches that of another drive (after cloning one volume to another), then while the system may still use it, services that rely on it for identifying the drive may have problems. It is possible that Time Machine could confuse two similar UUIDs in this manner, especially if multiple utilities and operating systems have been used to manage partitions on a system's internal drives.
To check the UUIDs of the volumes on the system, open Disk Utility followed by getting information on each mounted volume. In the window that appears you will find data and statistics on the drive, with one entry being the UUID. Compare these between your various volumes to make sure they are unique.
Additionally, this problem may be rooted in corruption in the Time Machine preferences file, which holds all of the volume configuration information for the service. Corrupt preferences is a common reason why programs and services stop working properly, and removing the preferences so they will be rebuilt from scratch is an easy and recommended remedy. To do this for Time Machine, first go to the Time Machine system preferences and make a note of the backup drives used and the list of excluded files. Screenshots are an easy way to do this.
Then open the /Macintosh HD/Library/Preferences/ folder and remove the file "com.apple.TimeMachine.plist" and restart your computer. This will cause the Time Machine service to relaunch and recreate its default preferences file. After doing this you can refer to your notes on your previous Time Machine configuration and add the destination drives and exclusion list items again accordingly.
Even if not everyone is affected by this bug, it does serve to remind us that there may be odd quirks with any backup system, so it is always best to regularly check your backup routines, and consider using multiple approaches to your backups (for example, drive cloning in addition to Time Machine). In addition to making sure your backup services are set up correctly, be sure to check the destination drive or drives themselves to make sure they are not experiencing any errors, by using Disk Utility to run a format and partition table verification.
These options are especially key as your storage setups expand and get more complex. Often people start with a single drive and then slowly add more storage and migrate their data to larger setups (both internal and external), and over time can build quite elaborate drive setups. As this happens, making sure the data gets properly managed with whatever backup approaches are being used becomes more important.