Hello John,
With the Madeleine sample set loaded, please first check that the polyphony limit setting is still set to its default of 256 (which is the maximum that the Free Edition allows) on Hauptwerk's 'Audio, MIDI and Performance' large control panel ('View | Large floating control panels (for this organ) | ...'. Even 256 might not be enough for big chords with lots of stops drawn when playing fast (but less than that definitely wouldn't). However, my understanding is that the Madeleine sample set only has five separate sampled combinations, so effectively the most you could have drawn at once would be five virtual 'stops' with it anyway.
With that done, if/when the problem occurs, do any of the meters on the 'Audio, MIDI and Performance' control panel go into the red?
One other point: audio only works for 75 seconds in the trial version of the Madeleine sample set, then it cuts out and you need to re-start audio/MIDI:
http://www.pipeloops.com/product_info.php?products_id=29
Could that be the issue? (Perhaps you're unintentionally loading the Madeleine trial version, rather than the licensed version.)