If they didn't provide a print out of the final results, it is all speculation on our part. They may have set them wrong from the get go and once you raised the ride height later, it just excerbated the problem.
Before you do it again, several things to consider, 1) have your chosen tire diameters set all the way around. If you have it aligned now and change tires, you will again add a variable which can impact alignment. 2) set you ride height were you want it and ask your specs to be set at that ride height, not the factory height. 3) when you provide your specs, point out they are in inches, not degrees. 4) requested a print out of the completed work so you can see how close to your request they were able to get.
You might look through your local phone book and find a chassis builder that makes oval track or sports cars chassis. Call them and see if they can do alignment or recommend someone who can. They typical chain store guys can read the book, twist the wrench, and align all the lasers to a tenth of an degree, but may not know some of the more intricate parts of making it work together and understanding why your asking for a deviation from stock. Sports car and oval track guys will get it and help you get there.