I believe I have found the problem Panda code.
In panda\src\glstuff\glShaderContext_src.I, the uses_custom_vertex_arrays function has been changed to always return true. In this case, most of my object with GLSL shader on them are no longer rendering. It looks like any object with a transform on it is not rendering.
If I revert the code to how it was in the previous revision, with GLSL shaders returning false and Cg shaders returning true, then the objects with GLSL shaders work properly as they did before.