what did you model it in ?
sounds like the issue was with the model itself.

here's a 40mm diameter flat based sphere I just knocked up in openscad. Should print without any issues. 3 shells and 0% fill will give you a nice hollow sphere :-)
40mm sphere.stl

You can easily resize it in makerware - just remember after resizing to hit the 'On Platform' from the Move options.
Amazing how many problems that prevents