Hi @jvarkevisser and sorry for the delay in my response.
Could you send me the model? If you have done it with Onshape then you can simply share the link from there or send me your CAD to jmurad@simscale.com and I will have a look at that.
A workaround would be to work with a so called “fictitious clearance (FC)” that removes the geometric information of the distance and that FC value will be taken into account.
Another option is to try it with other file formats like (STL, IGES etc.) - please not that STL might not be very “mesher friendly” sometimes but it is worth a try. Tagging @Get_Barried & @Anware here, maybe they have some additional tips for you I missed.
Cheers!
Jousef