Execute a command 20 seconds after the desktop is booted

As a workaround: simply create a script:

#!/bin/bash

sleep 20
synclient TapButton3=2

• Save it as something.sh, make it executable (for convenience reasons)

• Add it to your startup applications: Dash > Startup Applications > Add add the command:

  /path/to/your/script.sh
  

If necessary, you can experiment with the sleep 20 value; from your question, it looks like the command should be run after login process has finished (after it is reset by some process).

At the same time: it would be a more "clean" solution to find out which process makes the settings change, and fix that.

edit:

simpler solution: Add the following to your startup applications (Dash > Startup Applications > Add):

/bin/bash -c "sleep 20&&synclient TapButton3=2"