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This could be several things. Please try the following:
From your Safari menu bar click Safari > Preferences then select the Passwords tab.
Make sure: AutoFill user names and passwords is selected.
If that was already selected, make sure your OS X software is up to date.
Click your Apple top left in your screen.
From the drop down menu click About this Mac
Make sure the Overview tab is selected then click Software Update.
Your Mac may restart several times during the update process. That’s ok.
Then see if Safari autofills login data for you.
If there are no updates a available, you may have a Safari extension or third party plug-in installed that's causing a conflict. It's easy to troubleshoot.
From the Safari menu bar click Safari > Preferences then select the Extensions tab.
If there are any extensions installed, uninstall one at a time then quit and relaunch Safari to test.
If it's not an extensions issue, try troubleshooting third party plug-ins.
Back to Safari > Preferences. This time select the Security tab. Deselect: Allow plug-ins.
Quit and relaunch Safari to test.
Please take these steps to resynchronize the iCloud keychain. Your keychain on iCloud and your other Apple devices won't be affected. Take Step 2 only if Step 1 doesn't solve the problem.
Back up all data.
Open the iCloud pane in System Preferences and uncheck the Keychain box. You'll be prompted to delete the local iCloud keychain. Confirm—the data will remain on the servers. Then re-check the box.
If you still have problems, uncheck the Keychain box again and continue.
Triple-click the line below on this page to select it, then copy the text to the Clipboard by pressing the key combination command-C:
In the Finder, select
Go ▹ Go to Folder...
from the menu bar and paste into the box that opens by pressing command-V. You may not see what you pasted because a line break is included. Press return.
A folder named "Keychains" should open. Inside it is a subfolder with a long name similar to (but not the same as) this:
The above is only an example; yours will have a different name of the same general form.
Drag the subfolder (not the Keychains folder) to the Trash.
Restart the computer, empty the Trash, and re-enable iCloud Keychain.
Try these and we will go from there.
Thank you. This is a process to narrow down exactly what happened. Update me with the
results when you are done and we will go from there.