If you can post a sample scene showing your problem, I would be happy to debug it. 
Can you save that scene for Max 2010?
While I was testing this on my own, I found that when the PF Source’s Viewport % wasn’t 100% weird stuff was happening. You should see if that helps you at all.
I tweaked your setup by checking Position, ID and MXS Float in the PRT Loade Update operator and it seems to be working.
From my testing it appears to not work when the ID channel wasn’t being updating in the PRT Loader Update. I’m not sure why this is, but for now just leave ID checked in the PRT Loader Update at all times.
Bobo pointed out that I probably saw the channels as un-checked since the channel list was cleared when I changed the path of the PRT Loader’s files. Are you having any luck?