"It is clear that their traffic management identifies all encrypted data - not just P2P- and since they have to open ports for other encrypted data that would be the second best solution to get it to work."
The Ellacoya switches don't work as you would think. Whilst the switches can look solely at protocols and port numbers, they mostly look for application signatures to classify the flows. If the world ran p2p servers on tcp/80 they'd still recognise the traffic and classify appropriately.
The 6.4 software is still not classifying certain applications correctly. PN need to manually identify which applications are affected and implement a workaround on the switches to classify appropriately. If the signatures are particularly voluminous then it might be easier to use protocol and port numbers to identify the traffic. If you know of any apps/games that have been manually added, it might be worth running your p2p software on those ports to see if it improves speeds.
TT