Knowing where it came from, it is entirely possible that it was intentionally modified to function this way from the start. It's also possible that something has failed. Don't know, but it works fine with two 1/4" patch cables into a Y headphone splitter, except that renders the pickup selector switch on my Series bass useless except for the switch positioned with 'both' pickups on. Of course, then I can just use the Volume controls for each pickup to mix... which works fine too. But any other switch position 1, 2, or 4 is dead. (don't laugh - I had a Volkswagen once that wouldn't start unless you turned the headlights ON.)
Again, each output jack, whether out of B or T works fine individually, but activates only bridge (T) or neck pickup (B) when used like you'd normally use a DS-5 in mono mode. I think they are both on, all the time. So I think if I had a real mono/mono male > mono female Y-adapter, it would work correctly, and my basses pickup selector switch would work too. But, I digress...
Yeah... it's a puzzle. If I can get around it with a simple solution, that'd be great.