Why won't makerbot accept an STL file from Blender?
Here is what I suggest you try. If you have a file that you can view/edit in blender I would export it as both STL and OBJ formats. Then take those files and upload them to Netfabb (https://netfabb.azurewebsites.net/) and get a "repaired" file. Have the library try again with the repaired STL and OBJ files. If this doesn't work try to get the exact error message/dialog that the makerbot software is giving them as well as the version of the software that they are using.