With another lens attached switching between AF & MF on the lens causes the icon to appear / disappear. With the "broken" 50mm lens attached switching between AF & MF has no effect and it appears that it always thinks the camera is in MF (which is how it behaves hence my suspicion that this is the root cause of the problem, that the 100d for some reason is not getting the switch into AF).
With the Canon EOS EF lens system the switch is purely in the lens. There's no "AF/MF" or "On/Off" switch (hardware or software) for AF in the body on Canon cameras (like some other brands do it). That data is communicated to the camera over the same serial data pin that things such as lens info, aperture position, etc. are communicated.
The contact circled in red is the lens-to-camera data connection. The blue arrow is the data power supply pin and the yellow arrow is the data power supply ground.
If the lens is successfully communicating the position of the [AF/MF] switch to other camera bodies, then the problem is probably in the 100D camera body. My guess is that for some reason your 100D is not properly interpreting the signal it is receiving from the lens. It could be hardware related, but since other lenses work with your 100D, my inclination would be to think it might be due to a glitch in the camera's firmware related to information stored there specific to that particular lens or to STM lenses in general.
If you're not running the latest version of the firmware for the 100D, you could try updating to the latest version and see if that helps. Of course updating firmware always involves a slight risk. If the problem is hardware related, updating the firmware won't solve your problem. It might even make it worse.