I used to have a full scorpian system, (mk2 one so from downpipe back). I have basicaly cut it up to work with the vr. Its a bit of a mix of scorpian middle silencer + backbox, 6 branch, decat, and then powerflow pipe work to join up the silencers again. Take a look at the underneath of the car a page or so back.
Sounds either like dodgey welding or rust to me. My first thought would be engine movement but like you say you have a standard manifold so you shouldn't be have issues.