Yeah, the stl converter can be probkematic for translation to other platforms. To be fair, they dont advertise as "your 3d printing solution"!!!
I can help you out. You can run your output into meshlab and look at the result. Usually you'll need to run the unify normals filter. Then save it out.
If you can post an example, i'll take a look at it with you.
There are other options if you want to, or have to do this alot. I personally use another software (which you have to buy), with the best mesher in the business.