I'll be honest, I'm not entirely sure. Your design looks well enough to achieve 100% transport - stations are placed well enough.
I compared your double path with one I built in my own park and I see your green lines are separate - despite your paths being visually squished together in one big plaza. On mine, it's very much a solid green line. For the sake of experiment, try putting a path crossing where I put the red circle to connect your paths. Hopefully it wont ruin your design (I suggest saving your game). It probably wont work, but its worth a shot. It's all I can think of.
Another thing to check might be guest crowding and guest distribution - but I don't think that's the issue here.