It is possible that up to the last 30-40 seconds of a recording may not be present in the final stored file. This is because when you record signals with the GSS6400 there is a buffer that stores the data before recording it to disc. When you stop recording the 'stopping process' will cause the ‘not yet full’ buffer to be discarded. So it depends on how full the buffer is when you 'Stop Recording' as to exactly how much data, and hence playback time, will be missing in the file stored file. A nearly full buffer may be ~30 seconds, a nearly empty buffer is more like ~5 seconds.
In most cases users will be recording long duration files and so missing up to 30 seconds is not usually a problem. But recording short files, such as a 5 minute duration, it is recommended that you allow for up to an extra 30 seconds before stopping the recording process.