Sounds like you might have two 'problems' going on, you need to isolate which thing is causing which 'problem'.
1.
You're confused why the signal would be quieter from an amplifier when the volume is at 11 o'clock. On low-gain, the gain of the magni 3 is only 6dB which is subjectively a little less than twice as loud (10dB is percieved as approximately twice as loud). This is only achieved when the volume control of the magni is maxxed out. The volume control on the magni acts as an attenuator, so at 11 o'clock it might be attenuating the signal more than -6dB before it gets to the +6dB amplifier. Therefore overall you don't have any gain, you have attenuation - the signal coming out of the amp has a lower volume than what came from the laptop. There is still merit to using an 'amplifier' like this because the amplifier likely has lower output impedance than the laptop, so it is better at driving the headphones even if it is not actually making them louder. It is also good practice to have the laptop set at a reasonable volume even if you're listening quietly with the magni's volume dial turned down, as this optimises the signal to noise ratio between the laptop and amp.
If the magni is still quieter than the laptop when you have the magni's volume dial at maximum, perhaps it is faulty, otherwise your problem might be related to:
2.
Something other than the cable has been damaged when you stepped on the cable. Perhaps the jacks in the headphone, perhaps the jack on the amp, perhaps the cable shorted out internally and something was damaged electrically in the amp. Also check the cable going from the laptop to amplifier, since that cable is only used when you're using the amp I assume.