What Database are you using and what schema changes are not showing up. In my experience with SubSonic I have never had any schema changes not show up in the generated classes. The largest error that I have seen people make is to add a table to their database, run the SubCommander to generate their classes and then forget to include the generated class in their project.
The only other related issue I have seen people make is if you generate your classes in a seperate class and they are all generated in C# and the project that is using the classes is written in VB. VB can not read into a C# project so you first need to build your C# project to see the schema changes in your VB project. That is one of the limitations of VB.