Jon,
There are two things you can try:
1. Try doing your base painting in acrylics. In Shep's book, he actually talks about base painting in acrylics. If your thinners aren't too strong, they won't lift the underlying paint when you brush the thinners on. I've tried base painting in enamels and then spraying on a protective barrier of acrylic clear. The problem with this technique is, if you miss any areas spraying on the protective barrier (like corners), you'll have painting flaking off again from the thinners.
2. If you base paint in enamels, you could try an acrylic wash. Acrylics are a little harder and less forgiving when used as a wash. The trick is not to flood the model with the wash but only apply the wash in specific areas (like panel lines).
I actually base paint in acrylics and do my washes in acrylics too.
Jesse