Yes. Same problem, changing the preference in Preview does not help. The issue is with the dpi setting stored in the JPEG image's EXIF data. If the image is set to 72 dpi, then it opens at full size. If the same image (same image data) is set to 144 dpi, then it opens in Preview at one-quarter size (1/2 height x 1/2 width). The "1 image pixel = 1 screen pixel" setting is not being honored.
If the image is 1000x1000 pixels, then I want Preview to open it and use 1000x1000 screen pixels, regardless of the DPI setting of the image, which is really only relevant for printing. Preview is not honoring this setting on OS X 10.11.3.