That's what it sounds like. Thud. Unfocused and a little out of tune, especially around the F in first position.
Full disclosure: This happens with every non-steel string I try, including velvets of many varieties. I have widened the nut/bridge slots. Gut G's sound beautiful on my old girl! The danged old D just poofs around F in first position. Higher up it gets focused. This is also a brand new gut D, been on for about two weeks. Any ideas what causes this?
Try it on another bass. If it acts the same the string is a dud, if not you've got a fingerboard thing, a string tension thing, a soundpost thing, a wolf tone, or something like that.
What size did you get? I've found that lighter D strings are more focused. Also, the Gamut Pistoy D is MUCH more focused than the Lyon. The Lyon has a bigger, fatter sound. Pistoy is more expensive though. I used to use a light Lyon D and now use a light Pistoy D with great results. The Pistoy D sounds very close to a lower pitched G. (I just re-read that paragraph. It reads like English isn't my first language. Sorry.)
The problem you have sounds more like it's your bass and not the string though. You may need to work with a luthier to solve this one.
Plain Ds do tend to be like that IMHO (I had tried a Lyon D with thuddy result even on a very good old English (attributed) bass and on a very good quality hand made modern bass by B Puglisi). A Dlugolecki D also tended the same way and the standard Chorda D as well, BUT the Pistoy is very clear and full sounding and true pitch - recently got a C Henriquez Chorda set and on first try after a couple of days all the strings are clear and easily playable, pizz or arco, and seems to let the bass resonate easily.
Thanks for the help guys. Going to consult my luthier on this one. The fact that it happens with every no-steel string makes me think it's a set-up issue, not so much a string issue. I'll keep ya'll posted.