Without entering the fuel octane debate again,
just use whatever it says in your Owners Handbook,
and you won't go far wrong.
I'd be surprised if an updated Tune made that much of a noticeable difference.
( I have been surprised before though ! )
If have heard of Throttle bodies not being refitted properly,
allowing air to be sucked in, and this just
might be what you are experiencing,
so when you take the bike back in, ask them to double check the fitting / sealing
of the transition piece connecting the throttle bodies to the cylinder head face too

