I am LOST when it comes to gears and transmissions, but I know that on the TW, chain tension plays a HUGE role in shifting! I can always tell when my chain needs adjustment; shifting will become difficult...lots of neutrals, etc.
A few weeks ago, I noticed that the shifting was getting sloppy, but the chain was within limits...ended up being a worn front sprocket!
When I used a standard chain, I would have to adjust it weekly (I put a LOT of miles on!) or the shifting would suffer! Now that I have an O-ring...shifting is nice...until the sprockets wear!
Hopefully this is where your problem lies...