Here's the description of what you get for $95. Description from their site, titles from me.
Basic Tuneup:
If you're just bringing your bike out of winter storage for the spring or are a hardcore rider prepping for a race, <Bike Shop's> basic tune-up will get you rolling. This tune-up includes adjustments to the brakes (disc brake bleed add $15 per brake), gears, headset, bottom bracket, and hubs. Our mechanics will also spot true your wheels and lube the chain and cables for smooth operation. Parts and accessories installation is additional.
Fancy One (the one we got)
This tune-up takes the basic service a couple of steps further. Included are inspection of your frame and components for wear, the removal of your chain, cassette, and crankset for cleaning in a solvent tank, cleaning of components, and cleaning and polishing of your frame. We also check the suspension components on mountain bikes. Parts and accessories installation is additional.
To be fair, both bikes are now very very clean and pretty. And I don't want to completely bash the bike shop - a mere two days ago I would have been singing their praises. But I am pretty disappointed. And I did specifically ask them to look at the shifting.