After playing around with this for a while, it seems there is a problem with the Web pages when using Pocket IE.

I am able to stream PocketPC - IPAQ standard files. The issue seems to be that when you select a file to watch in Pocket IE it always tries to play the file from the Primary Store. It's kind of strange the way the watch page is displayed in Pocket IE, in that the tabs are not displayed. It is just a list and I was scrolling down to the PocketPC part of the list and selecting the entry to play. I noticed that it always plays the corresponding file from the Primary store. So just to test it I moved a show from the PocketPC directory to the Primary directory and was able to stream it to WMP 8 for PocketPC.