Thanks for the reply Billgwx. The sound of the thump itself would be fine, it's just that it's different than the other strings, and lines that skip between sound awkward.
I've got a few photos that show the bridge saddle, tuning peg, and nut, which may help to explain what's going on.
I'm hoping this is an easy fix and I can get on with enjoying this bass. Worst case I'll return it to the store and keep hunting for another bass in this series. They're oddly hard to track down in my region.
(sorry for the huge images - I'm a bit of a tech weakling)