This would be a damn good reason to stay away from this incompetent dealer.
Of course PADS can access the ECU, and before the service code was discovered it was the only way to reset the spanner icon.
I suggest you now relearn your keys without the help of PADS. You were on the right track some time ago, but didn't present the second key. If you go into "MENU", "SERVICE", enter the service code, and then select "CODE RECOVERY". It will ask you to insert your two keys, and then offer the chance to change the user code. Since your keys had different codes assigned to them, this is your chance to make amends.
Good luck.