Sounds like a bunch of fine print BS from Specialized, i.e., a 5 year warranty that goes to any extent not to apply in any given situation. Like this from their website:" : ICAUTION! Be sure to wipe the shock body clean after every ride to prevent wear and damage to the shock. Failure to follow this caution will void the warranty." In the '09 suspension manual I scanned (72 pages!), no other service beyond this cleaning was required by the owner until 50 hrs. I would call (preferably) or write Specialized directly about your situation, try to get to someone specializing in unhappy customers. Be sure to review the applicable manual first and assure them that you followed the directions to a T and say you do not understand why the wonderful 5 yr warranty does not apply. OTOH if your supersize nephew borrowed it and hucked it all over creation, just pay the bill and don't loan it to him anymore.
$90 doesn't sound crazy for a tune-up, though I hate those kind of terms that don't really say what they did. It should be itemized. Many shops provide free adjustments as "service after the sale". But it looks like Specialized may have followed the car dealers' example and specified service by an "authorized dealer" at specified intervals to keep the warranty in place.
I had a hairline crack develop on a Bianchi roadbike crankarm - it was out of warranty but they covered it anyway (the shop handled it for me with a little prodding). Took a while to get it, but I was like jeezum, I've had cheap cranks last for years without problems, I should not have to pay to replace a pricey crankarm a year or so down the road from normal use.