Could be S3D's thin wall behavior. Sometimes dropping the nozzle size setting from .4 to .39 can force it to slice areas that otherwise it doesn't or at least let you know so you can fix it in the model. Makeprintable will be launching a new version after the 19th that is supposed to work better with thin walls also.
Another thing to try is the "Merge all outlines into a single solid model" option. This is can help.