Great job. this new version fixes a number of issues.
About JPG-XR, however, it seems that no parameter is taken into account in beta 1: whatever the value of quality, internal color format and block filtering, the output is ever lossless (i.e. as if with quality 100, no chroma subsampling), as checked by comparing the .JXR with an initial .BMP image.
By the way, it seems to me that chroma subsampling in JPEG and JPEG-XR are similar, at least in principle. Currently the labels are YUV444, YUV422 and YUV420 in JPEG-XR, and (1x1,1x1,1x1), (2x1,1x1,1x1) and (2x2,1x1,1x1) in JPEG. IMHO, It should be preferable to use the same labels for consistency.