i just installed mine a couple weeks ago with ryan and mike... it seems like you have the s pipes on the wrong sides.. i think if you just switch them it will correct this problem

 

They are on the ridges of the flanges on the S tubes.

 

ok the only dots i have on the flanges are 4 dots on both flanges....

 

Yes, on the Stube flanges and on the flanges of the magnaflow resonator. I can't remember off the top of my head but I think, 1 tube has 1 dot and one tube has 3 dots. On the resonator one flange has 2 dot and one has 4.

Basically the flange with the 4 dots mates to the tube with 1 dot and the flange with the 2 dots mats to the tube with 3 dots. If I remember correctly. They are definately there, they may be a bit worn off yours.

Also I looked at the picture really closely and it appears the flanges are not perfectly aligned. When your done, each flange should fit perfectly flush against the one its secured to.

Can you post a pic of how you have the pieces put together?

EDIT = Even better, found the install instructions from Tony at FI emailed me a while back. Enjoy

http://www.thedunphys.ca/G35/G35CatBackInstructions.pdf