I just moved to 1.0.3 and I've done several test builds. In one of the builds, I removed a project directory from the working directory to test out the Changes section in the build log. When I ran the build again, Continuum checked out the missing directory just fine. After the build, in the e-mail and on the web interface, the Changes section shows 3 blank columns and then the files that have changed in the 4th column.
I think it may be broken again. _Mang