I have yet to experience any advantage of the Ric twin truss rod system, be it old or new. It is in the best of cases as stable as a Gibson or Fender truss rod, but in most cases it is not. That you would need to adjust one truss rod different from the other I have never encountered. On five Rics I own neither the necks are warped enough or the fret job is uneven enough to necessitate individually different adjustment.
I think that neck stability is more a matter of neck woods and construction, than it is the truss rods.
In difficult cases, John Hall suggested tightening the rods like you would tighten old-style folded rods, i.e., pull the headstock backwards with your hand and then use the rods to "lock" the neck into position.
Did you check the body-end part of the rods? Perhaps the acorn nuts are sinking into the wood?
I have many times in the past adjusted the rods slightly different, most of the times it was when the bass side had a slight curve and the treble side was straight.
Another advantage of the Ric truss rods, old and "new" (post '85), is that you can easily pull them out, fix what needs to be fixed, then insert them back inside the neck. This can be done on your kitchen table, no need for special tools. You can't do that with a Fender or a Gibson.
Here's another idea. When you pull the rods out you can see that they are curved. This was done in the factory. Don't attempt to straighten them. In some cases the rods "flip over" inside the channel and the curve is in the wrong direction. I did this with my Shadow: removed the rods, then inserted them back inside making sure the curve was in a back-bow. Until I did that, I had to use TI's because of the low tension. Now I use medium gauge DR's, the neck is dead straight - zero relief - and very stable.