The software merely sends a command to the gearbox ECU, it's the gearbox's ECU that's doing all the number crunching - NOT the laptop.
All the laptop is doing is instigating the procedure.
With that in mind - follow the procedure again, I've added some extra info, I hope it helps.
1: Turn key to MAR, start Alfa Diag, select CLUTCH SELF ADJUST and run it (For MES, it will finish almost instantly - For AlfaDiag, maybe it hangs such as yours did..? I haven't done this with Alfadiag so I don't know).
2: After you press the execute button (ignore the waiting bit) - Turn key to OFF, wait for all lights to go out.
3: Turn the key back to MAR, wait for all check lights to go out, select 2nd gear, press the brake pedal, Start the engine.
(at this point, the gearbox will return to neutral as you turn the key to start - this is normal.)
4: With the engine running, re-select
2nd, accelerate with the pedal to the floor till the RPM passes 3000rpm, slow to a gentle stop.
5: Turn key to OFF, wait for lights to go out, start engine and drive normally with a nice smooth clutch.
Just remember, once you press the execute button, you can unplug the laptop if you want.. ignore the messages it throws out.
All that said, if the system is as smooth as you say.. then why mess with it?
As an aside, I'd buy myself a copy of MES
if I were you. Alfa Diag works, but its old and outdated.. and I dont think its supported any more anyway ( in regards to software updates)
Also, I didn't write this guide, the ever knowledgeable Smaky wrote it and it's never failed me or anyone else using it.. trust in the guide!