One thing that'd at least help diagnose your problem would be to put a single dense cable between your sending P2P tunnel and the Controller, so you can see exactly how many channels are going through it. My guess is that either there's another P2P tunnel connected to that one on your Controller that you set up and are sending a bunch of channels through and forgot about; or the problem exists where your dense cables are branching off into smart cables, and one of them has too many channels trying to go through it.
Try sending your P2P tunnel through a dense cable before it connects to the controller, then see if that doesn't help you figure out what's going on.
Right now my system is pretty basic and i dont have many lines yet. The weird thing is i have a P2P on two different faces on the controller, one of the faces is for crafting the other is for my Thaumcraft area, both of those P2P are connected on one line but the TC side only is using one channel on this line.I didnt change any of the channel useage on the line but i connected the P2P for these MA/Interfaces to the thaumcraft P2P with the memory card. The main line is still carrying the same amount of channels(6 P2P's) but i just took one channel off one P2P and put it to another,i only have 8 channels period being used on my whole contoller and thats divided between 3 different sides so nothing should be full.