Apologies, wrong patch. This is the correct one.
--- openjpeg-1.5.2/applications/codec/convert.c.orig 2014-03-27 11:58:06.000000000 +0100 +++ openjpeg-1.5.2/applications/codec/convert.c 2015-02-11 00:53:46.000000000 +0100 @@ -243,7 +243,10 @@ if(fwrite(&pixel_depth, 1, 1, fp) != 1) goto fails; - image_desc = 8; /* 8 bits per component. */ + image_desc = // bits 0-3 are # of alpha bits per pixel + bits_per_pixel == 16 ? 1 : + bits_per_pixel == 32 ? 8 : + 0; if (flip_image) image_desc |= 32;