It depends on the tool, and newer versions are better at backing out some changes. In general its probably better to start over and test a few at a time to see where the issue is, and might be a good idea to look at automating building it so you don't have to worry about when you do need to rebuild it. Take a look at
For a good article, I based my work of his.
In regards to some of your issues your seeing, I'd start with a test pool without the optimization tool ran and one with and nothing else to rule out anything else. In general the optimizations by default shouldn't cause issues with a base windows install, its when it runs into other customizations you need to make.