This is a sample 16bit CMYK TIFF with 2 alphas, as generated by Adobe Photoshop. This is a much simplified test case, but demonstrates consistently what I'm seeing with our live files.

If I run the following ImageMagick command I get bad results:

convert -colorspace RGB cmyk16multialpha.tif cmyk16multialpha.jpg

Both input and output files are linked above and in the file attachments list below.