I'm pretty far from being any kind of expert when it comes to wiring...or anything else for that matter...but it sounds like your current "black box" may be malfunctioning.
If you do as you say, & snip the wires to the existing trailer wiring harness & install a new one, this theory could be proven, one way or the other.
Also, it could be as simple as corroded connections on the one that's there. Maybe a poor ground connection?