Nothing odd really. It is your settings.
1 - you set the file bit depth to 24 bits. This means that anything coming in will be recorded as that. Of course if the input has only 16 bits of true info, the last 8 bits will probably be zeroes.
-- an advantage of this, on the 744 you can have 24 bit resolution on the analog ins even if you simultaneously record a 16 bit digital in from another source
-- only issue with this is that you waste a bit of hard-disk space. Generally there is plenty anyway
2 - the digital input is smart and tries to lock to whatever you send in there. This is most sensible really, saving a lot of hassle. 16, 20 or 24 bits it will simply lock (20 bits used to be rather common)
3 - the sampling rate is "overridden" by the digital input. I am not sure about how large the locking window is. Assuming your external equipment is nominally 48kHz but really runs at 47kHz. This, in this respect, very large difference may be locked to or not, I am not quite sure. With normal "errors", say less than a percent the SD recorder locks fine (in my limited experience).
So all in all, nothing odd is happening, the machine simply does its best at doing what you ask it to do.
Gunnar