If the core is idle (that is, it is not loading, processing or unloading any frames), it waits for either frame data or configuration data to decide what action to take next. If new frame data is seen by the core control module without new configuration information being seen, then the core starts to process a frame using the existing configuration. If configuration information is seen before frame data, or on the same clock edge as frame data, then the configuration is applied to that frame.
To ensure that the configuration data is applied before the frame is processed, the configuration information should be written to the Configuration channel where the write of configuration data to the Configuration channel must complete at least 1 clock cycle before the write of the first Data Input channel. Failure to do so can result in the frame being processed with the previous configuration options in use.
Perhaps the easiest way to satisfy this in a system context is to configure the core before enabling the upstream data master.