Hi Chris,
It's not a straightforward fix in the splitter however I'll see what I can do. I think if I make the cache generation compulsory it will be possible to handle this without too serious an impact on performance.
I understand that this would require deferring the writing of the nodes until the whole input (nodes, ways, and relations) has been consumed. I would greatly appreciate a fix. After that, it would be time to have the Geofabrik dumps corrected. By the way, I think that you should restrict this inclusion of all nodes only to select relation types (only multipolygons come to my mind). For instance, route relations (such as the international E road network) should be clipped at the tile borders. For what it is worth, here is my attempt at implementing this workaround: MM> A fairly cheap work-around in mkgmap could be to discard those ways MM> whose resolvable nodes completely fall outside the bounding box when MM> some of the nodes cannot be resolved. It did not make the warnings for the two other multipolygons go away. Marko