Further to Cedric and Christo, any malfunction in this area, should show up on your boost gauge (if you have one fitted

). According to Cedric's explanation you will be over boosting, and I am pretty sure you will feel an increase in power.
This is where your gauges are critical. Boost and EGT should show any malfunction of injectors, combustion issues and turbo problems, along with what the exhaust is telling you in the form of smoke signals.
To me, personally, that sounds like something "flapping in the wind", and starting to act as a valve in the pipe. In the absence of any boxes and possibility of internals flapping about, my guess would be the internal layer of the flex joint coming loose, and flapping around. Is quiet at start up, and only starts gets noisy after revving? I would venture to say it has started separating from the side closest to the engine, a good rev bends it over toward the back of the pipe, after which the flow in the pipe prevents it from returning to its original position, and ends up flapping. Bet that if you switch off the engine, and then restart, the noise is gone till you rev it the first time...
Well thats my wild guess at your problem, hope you get it sorted out with minimal damage to your wallet, not that those 3" flex pipes are cheap. Mine cost me R900, seven years ago when I did the Sani.