Trying to run the default SpatialAnalysis Tool in Portal 10.6.1. I get the same error message with both web maps and web apps. Both internal and external apps otherwise work correctly (so, basically, they are fine if they don't need to use this tool). ESRI tech support is stumped (though we will continue to try random fixes again next week).
And if it helps, pasting the URL directly into a browser does indeed find the page.