Time machine backups no longer include hidden system folder like /usr and /sbin

My Time Machine backups Aug - Oct seem complete.  When I look at them I see all the expected folders and files.  Starting in November key system folders disappeared: /sbin, /usr, /bin, etc.  However, the non-hidden one are there: /Applications, /Library, etc.  Later in November certain things show up again like /usr/share/man/whatis and /usr/share/man/ri, but nothing else under /usr/share.  I've looked for all possible places where folders might be excluded and have found nothing.
I'm using Mavericks on a MacBook Pro with a Time Capsule.  All software and firmware are completely up to date.  I can't explain the behavior.  If I take one example I can see /usr in the Nov 5 backup and it is fully populated.  It is gone in the Nov 12 backup.  In the Nov 19 backup it is back but only with /usr/share/man/whatis.  There are no errors in my logs although my logs don't go back that far, so if something happened the week of Nov 5 I don't know.
Anyone with any guesses?
K-Family

If you have more than one user account, these instructions must be carried out as an administrator.
Launch the Console 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 Console in the icon grid.
Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left. If you don't see that menu, select
View ▹ Show Log List
from the menu bar.
Enter the word "Starting" (without the quotes) in the String Matching text field. You should now see log messages with the words "Starting * backup," where * represents any of the words "automatic," "manual," or "standard." Note the timestamp of the last such message that corresponds to an abnormal backup. Now
CLEAR THE WORD "Starting" FROM THE TEXT FIELD
so that all messages are showning, and scroll back in the log to the time you noted. Select the messages timestamped from then until the end of the backup, or the end of the log if that's not clear. Copy them to the Clipboard by pressing the key combination command-C. Paste (command-V) into a reply to this message.
If all you see are messages that contain the word "Starting," you didn't clear the text field.
If there are runs of repeated messages, post only one example of each. Don't post many repetitions of the same message.
When posting a log extract, be selective. Don't post more than is requested.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Some personal information, such as the names of your files, may be included — anonymize before posting.

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