Hi, Joe.
After much tearing of hair and taking the names of several famous mathematicians in vain :-) I have found a new algorithm for the map importer that fixes your issues on Lake Ontario (and several other places). I'm still resolving some corner cases for Lake Superior and Lake Michigan, but I hope to have them fixed as well in a few days. It's just painful that it takes 20 hours (!) to run the entire planet OSM dataset through the importer so I can check the results. I fixed most of the Lake Ontario issues using a map data excerpt for just the lake and its immediate surrounds, but even that took an hour per run.
Andrew, KA2DDO