Time Machine only backing up Users folder

Since upgrding to Mountain Lion my Time Machine is now only backing up my ~/users/ folders and not the whole hard drive like it used to.
Nothing is excluded in Time Machine settings.
Has anybody else got this same scenario? I'm wondering if it's an isseu on my MacBook or if it's by design with Mountain Lion.
Hopefully it's not by design as none of my Application Preferences and other files in Library are being backed up

My other Mac was fine, but comparing the com.apple.TimeMachine.plist files of the two machines reveals something interesting.
On the problematic Mac (Mac #1), before I deleted the .plist, all of the system paths (/Applications, /Library, etc.) somehow got added to ExcludeByPath on or around August 30. After deleting the .plist and starting fresh, the ExcludeByPath key and values are gone, as is expected.
But on Mac #2 (the Mac with no Time Machine problem), those exact same paths that were under ExcludeByPath on Mac #1 are specifically enumerated under IncludeByPath, whereas they are not specifically listed after starting fresh on Mac #1. (It's possible these existed on Mac #2 before my upgrade to 10.8.)
If the system paths were enumerated under IncludeByPath on Mac #1 prior to starting fresh, either the system, Time Machine, or another app changed IncludeByPath to ExcludeByPath. I cannot verify if IncludeByPath was in Mac #1's .plist because I no longer have the historical data.
In summary:
Mac #1 (Mac that stopped archiving system files):
.plist contained system paths under ExcludeByPath
after deleting .plist and resetting Time Machine, .plist no longer contains ExcludeByPath
before and after resetting TM, IncludeByPath was/is absent
Mac #2 (Mac with no TM issue):
system paths specifically listed under IncludeByPath

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Time Machine not backing up user folder

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Hi I'd like to jump in here. Your app showed me this:
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Hi.
I am having an issue with Time Machine on my MBP running 10.5.5. I currently have 2 TM backups on a 400gb external hard drive. Each backup is roughly 45gb. However, both times, my iTunes folder not been backed up. I checked the Time Machine options and nothing is being excluded.
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com.apple.backupd[621]
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HeinrichFromBremen wrote:
Of course not. But there is a difference between lack of perfection and deliberately building bugs into the software.
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How can i know that homeis the only omitted directory?
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A bit of an overreaction, I think, but your choice.
What would be the alternatives? tar? ditto? dump does not seem to exist.
See #27 in the FAQ link above. As far as I know, they all omit some things.

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I've tested these instructions only with the Safari web browser. If you use another browser, they may not work as described.
Triple-click anywhere in the line below on this page to select it:
{ diskutil list; echo; diskutil cs list; } | open -ef
Copy the selected text to the Clipboard (command-C).
Launch the Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window (command-V).
A TextEdit window will open with the output of the command. If the command produced no output, the window will be empty. Post the contents of the TextEdit window (not the Terminal window), if any — the text, please, not a screenshot. The title of the window doesn't matter, and you don't need to post that.

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Steve Holton wrote:
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Welcome to Apple Support Communities
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Time Machine only backing up Users folder

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