The mod done by VW had one of those alloy valves on each heater hose, joined by a small rubber pipe. I can only see one alloy valve on yours. Anyway, it's probably best to revert back to a straight connections to give a good flow. As luck would have it my matrix split a couple of weeks ago. I wasn't driving but the car had been sitting in traffic and overheating. Despite the coolant filler cap having a release pressure of 1.5 bar, the matrix burst. A bit of a mess, and anti freeze doesn't evaporate away! You can see the crack all along the top in one of the pics. The cause has been resolved; the rad fan cables have a plug and socket connection behind the n/s headlight and it had rotted away. I've now replaced the rad fan cables with ones straight to the battery, with soldered ring connections as a more lasting arrangement. Out of curiosity I dismantled the matrix. Here are some pics. The coolant flows in to one side of the plastic cap, down the alloy pipes, then back up to the other side of the cap and out of the return hose. The cap sits on a rubber seal all around the pipe ends and has a divider along between the flow and return pipe ends so I don't see there is chance for any coolant to avoid going around the alloy tubes. If you were getting a good flow both ways when flushing and you say a lot of muck came out, then I reckon the matrix should still be functioning OK. Try removing the valves in the flow and return pipes and see if that helps. I can't see any reason for the hot coolant to not flow through correctly. You will need to rev the engine a bit to get the coolant to begin to flow uphill through the hoses, but once it's started it should be OK.