Lightroom 5.4 seems to auto crop RAF X-Trans sensor files compared to both Photoninja and Aperture. I've tested on a few cameras and only the X-Trans RAW files seem to be affected by this. Also, Lightroom is still interpreting the X-Trans RAW files soft compared to other RAW converters.
Are you setting up cropping on the camera? For some cameras (the Fuji X100s for example, an X-trans camera) if you set the image size on camera to a cropped size, Lightroom will detect that and automatically use that crop rectangle. You can change the crop in the Develop module (for example to the full un-cropped raw size), and then later return to the "As Shot" crop using Lightroom's crop tool.
Unfortunately that isn't the case. The camera does not have any crop settings in place, and setting the crop factor to "as shot" in LR does not revert to the original image size. LR is definitely cropping the RAW files as they are imported. My non X-Trans camera RAW files are totally fine, so this is definitely an X-Trans RAW files specific issue.