With photos already in Lr, you would need Read Metadata From File to bring in those GPS details. With new images, you won't need to do this - unless there is still a problem with the metadata template you are applying in the import dialog. So make sure you have saved the updated metadata template.
One other detail is where are you looking for the GPS when files have arrived in Lightroom. There are two GPS fields - one is the EXIF field which is automatically written by the camera and is protected, while the other is an IPTC field which you can use to manually enter GPS details. The latter starts off blank, but maybe you are looking at it, not the EXIF field?
If you have Lightroom CC, you can use Lightroom Mobile to automatically import iPhone pictures, and it does preserve the GPS data.