This started when I moved my Windows OS installation onto an SSD drive. The SSD drive holds the OS, program installations, and all temporary files.
Because it is only 250 GB, my user files are stored on a pair of old fashioned 7200RPM hard drives configured in a RAID 0 configuration. This drive is mounted as "C:\users\%username%". I copied Windows generated contents into this "folder", and everything works fine. Except IE. It no longer showed any files in its "History" window. I moved its "Temporary Internet Files" folder to the SSD to get better performance, but its history window was still empty. The "Temporary Internet Files" folder had files, but they were just now shown in the history window.
I was running Windows 7 back then. So I figured that I would upgrade to Windows 8, and the IE problem would go away. Well it did not. Worse, Windows 8 installation did not understand that "C:\users\%username%" was not a regular folder but a mounted drive, and created a mess. I had to manually fix the mess.
The IE problem persisted. I was running a newer version of IE, but it still would not show any files in its history window.
Then I upgraded to Windows 8.1. The IE problem was still there. Windows 8.1 installation did not understand that "C:\users\%username%" was not a regular folder but a mounted drive, either. I had to manually fix the installation mess, again.
Yesterday, I saw this at "answers.microsoft.com": "IE11 no history displayed". It turns out that I need to have a "system" attribute set on "C:\users\%username%\appdata\local\Microsoft\Windows\history". Apparently when I copied my files to the drive mounting folder, the attributes were lost, even though I could swear that I used the preserving attribute option on the copy.
So I added the "S" attribute as suggested. Now IE history is working again. Finally.
The original answer was from "social.technet.microsoft.com": http://social.technet.microsoft.com/Forums/ie/en-US/6418ae13-63c7-44a1-9e97-0ad875a2bd7a/browsing-history-not-being-recorded?forum=ieitprocurrentver
Thank you Rory.