If your entity has the 'transparency' flag set to a value greater than zero and the entity texture has alpha in the diffuse, you will get transparency when lightmapping it. You can switch off an entities ability to cast a lightmapped shadow by setting 'castshadow' to -1. Both these flags can be found in the entities FPE file.
PC SPECS: Windows 8.1 Pro 64-bit, Intel Core i7-5930K (PASSMARK:13645), NVIDIA Geforce GTX 980 GPU (PASSMARK:9762) , 32GB RAM
