Extruder run differently with same configuration

Dear All,
Recently, I am working on building a delta printer which has a nozzle associated with two extruders.
It means the machine can allow one nozzle to extrude two different filaments.
The hardware has been installed well, but there are a lot of unexpected errors during configuring the marlin for the machine.
The attachment is the configuration.
The marlin passed the compiling.
the machine does work, but not correctly.
My machine has two same models of extruders.
I configured them by same parameters.
Unfortunately, They works differently when I tested them by Repetier-host.
I sent the command to ask them to extrude 100 mm filament.
the extruder 1 is OK, but extruder 2 always extrude more filament and run faster.
They were configured by same values and parameters. I don't know why they run differently.
I tried to switch the hardware of extruders to check if the extruders are different, but the result shows that the extruders are same.
Can anyone can explain this strange event? Thank you.
The attachment is my configuration.

Are the microstepping jumpers under the E2 driver port in place? Do they work?

Allso check the values are correct in the eeprom.

Dear O_lampe,
Thank you for your nice reply.
You really give me a hint to find the answer.
The jumpers and the values of EEPROM are OK.
I found that the problem is caused by a broken A4988.
I replaced the broken A4988 by a new one. Both of extruders work fine as my expect.
Thank you for helping me to solve the problem.