My brother recently got a Giant full susser from Halfords (£1000) through the cycle to work scheme. Halfords claim they can get any make of bike you want. Before you ask, Halfords is the only company he is allowed to deal with through his firms scheme.
It has a problem with the Bottom Bracket so he took it back and they've claimed it really needs to be looked at by Giant.
He's left them to contact Giant, but he did talk to Giant himself, and they are pretty livid that Halfords are supplying their bikes, and they're pretty keen to find out who has been supplying them!
They've said that the warranty is invalidated because he is effectively the second owner. Given that there is a 10 year warranty on the frame, this doesn't bode well.
He's trying to get his 'money' back from Halfords, and is contacting the company that operates the C2W scheme.
Just a warning if you're thinking of ordering an off-range bike from Halfords. Shit situation when you've been looking forward to getting your new bike.
Your warranty is with the re-seller - in this case Halfords. It's up to them how they deal with it.