I think Wayne may have picked up on something that I didn't in your post Peter - which is that it seems you may be saying you are now uneasy about the deal because of the appraisal. If that's the case I'd take a step back and make your own independent assessment. Here is an appraiser story...
I once bought a bank owned house. It was not marketed well and I got it for an absolute steal of a price. My lenders appraiser came in and said it was worth a few thousand more than I paid. One year later I was using the same lender on the same property to do a cash out refinance (a loan where you take out some of the equity that you have in a property). The lender hired the *same* appraiser who sent the *same* guy out to evaluate the house. With no major market fluctuations in my area that year, he said the house was worth twice what he did the year before - which was still a lowball figure.
Point being - the primary function of the appraiser is to make sure the bank doesn't get stuck with a property that is worth less than the loan made against it. So long as it's apparent that this isn't an issue, they will end up at or near the sale / loan price.
So all that to say I wouldn't let the appraisal swing you too hard if that is indeed the concern. Just make sure your confident in your rationale for the valuation that you made.