I haven't messed with the lightmapper for quite some time and especially as of late since I believe it's still being worked on, but are you using the PBR shader with D,N, and S textures?
Desktop: i7 4770@3.4Ghz (passmark 9809), 12GB RAM, Win 10/64, GeForce GTX 1080 (passmark 12006), 1TB SSD, 1TB HDD; Laptop: i7 4800MQ@2.7Ghz, 16GB RAM, Win 10/64, GeForce GTX870M , 1TB SSD.