I can connect OK from Stanza on the iPad. I would guess that it is probably your firewall that is blocking the connection. Are you specifying a fixed IP address in Stanza or letting it try and find the Content server automatically. I have found that the fixed IP approach tends to be more reliable.
Having said that I find that it tends to be much more convenient most of the time with the iPad to do USB transfers via iTunes to iBooks. You lose the remote access facility (as iBooks does not have it), but you get much better integration with Calibre.
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