I made a quick test converting a X-Pro1 RAW file into JPEG, TIFF and DNG in Lightroom 4.2, then converting DNG to JPEG in Bridge (Photoshop) and also viewing the DNG file in Photoshop. There were nothing wrong with the pictures, all identical.
Have you checked in-camera JPEGs (you can convert RAW file residing on the SD card in camera after the shoot) or converted the files with SilkyPix which comes with the camera. That way you can find out if it is the camera or some strange setting in LR which causes this.
Off Topic: The strange "watercolor" effect noticeable most easily in foliage is caused by pushing the sharpening amount slider past 25 in LR 4.2, by the way. The effect looks like the pseudo random pixel arrangement in the X-Pro1 sensor. The rumor has it that Fuji and Adobe are working on this problem together now.