Maybe I did something wrong then

I just ordered a PC for my dad from you guys, which was about $1,500 total. I did a comparison against how much the same parts were over at Newegg, and concluded that the markup was about $400. Based on all the positive reviews we've seen for Puget, we figured it was worth not having to go through the hassle of building one ourselves, or having to deal with Dell or one of its ilk, and to have some decent support as well.
So, based on this post, I thought the markup for a $3,000+ machine would be about the same or equal, so I started playing around with the Puget configuration tool on possible builds for myself. (I plan to get mine in a few months, so will probably hold out for Sandy Bridge.) When I got through, the markup on mine was about $1,000. (The SSD drive seemed to be the biggest culprit.) Does that sound about right for a $3,000 - $3,500 Puget build? If so, that's a little too steep for me. For $1,000, I'd rather just build it myself (or pay somebody here locally to do it), and risk having to RMA a part or two.