Nobody has found this problem on his camera?
Problems like this almost always amount to user error. Read the manual.
In fact, I'm having the same problem. I'm pretty confident in saying it's not
When When Adjust by Lens is selected, powering off then on resets the setting (or W/T settings for a zoom lens) to zero, and also clears out a manually entered lens serial number. If I set it to All by Same Amount, the setting entered is retained...but, powering off actually changes the setting to Adjust by Lens, which is zeroed out. Even setting it to Disable and power cycling results in it being set to Adjust by Lens.
The same reversions occur if the camera goes into standby mode - when it's woken up, the AFMA setting, regardless of where it was left, reverts to Adjust by Lens with the previously set value(s) zeroed out.
This occurs with several lenses (zooms and primes), and occurs in any mode (standard modes as well as the C1-C3 user settings).
I called Canon Tech Support, who had no information on the issue, but the tech rep indicated that he tried it on a 1D X and it didn't display that behavior.
I expect a forthcoming firmware update which, "Addresses an intermittent issue that..." I can't see how it can be anything but a firmware issue, and I would bet it's a bug triggered by other settings (e.g., people who enabled the C2 and C3 settings before applying AFMA see the problem, or some other odd combination.
Mine has Firmware Version 1.0.2 - I wonder if there are cameras with different firmware versions in the wild?