I agree with Tim that as soon as lawyers and politicians stuck their noses into things (under the disguise of "protecting the consumer") that it became much more difficult. Lenders developed working relationships with appraisers who were fair in their opinions, reasonably priced, and got the job done promptly. Of course there were shady characters out there who took bribes and inflated values. Those few bad apples ruined things for everyone.
At some point it became a bad thing for realtors, lenders, appraisers, etc to work as a team. I personally don't get it. Making money is not a bad thing so long as you're not taking advantage of people.
Now lenders have to randomly assign appraisals to a pool of approved appraisers and what you get sometimes is someone who is less experienced in that given area. A generalist as opposed to a specialist.
In terms of the low-ball appraisal, is there hard sales data to support the values of your purchase contracts or does it heavily rely on adjustments and out of area or out of date comps?? If there is hard data and the appraiser chooses to ignore it then you have a real problem. Good luck appealing an individual appraisal. In my experience it is often fruitless and you need to have an iron-clad case with several better comps in order to have any shot.
If this is a frequent problem then I would get together with your broker, fellow realtors, and/or the local board of realtors and approach the lenders about improving the appraisal process and potentially eliminating this appraiser. Provide as many examples as you can. Complaints from one agent is going to sound like sour grapes, but banding together as a collective could get your voice heard.