MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
yes tried it with the same fan, and I agree its a very tight fit.
But I guess my fan was a little used and the rubbery corners are long gone, sorry I did not thing of this.
To rescue the print you could remove/cut the bump and use some (hot)glue secure the fan.
I will upload a fixed version