A Physical Configuration Audit (PCA) is a Configuration Management (CM) audit that verifies that whatever you have built conforms to the technical documentation that defines the build. What that means is that CM must compare the configuration of the as-built product to the design documentation of the product. For example, CM looks at the list of all the configuration items (versions, etc.) in the as-built product and compares that list to the list of what is supposed to be in the product.
A Functional Configuration Audit (FCA) is a CM audit that verifies that the functions of the as-built product match the baselined functional requirements and that the operational and support documentation is complete and satisfactory.