Ragnor: It seems to be Reach or upstream rather than a Telstraclear transparent proxy issue.
Lucky no one is holding their breath.
It was never a Transproxy issue, my traffic was sFTP over SSH (port 22 and port 2222 - neither made a difference) - end to end encrypted, not proxyable.
Incidentally, last they contacted me, TelstraClear were trying to set up a test bench off of a cable modem in Wellington, because they could not replicate the problem properly elsewhere. That suggests to me the problem may be closer to home than Reach.
I have no idea if they did set up their test bench, or if they conducted further tests, however, the problem remains, and may even be a little worse, so clearly nothing has been done about it.