I've been having this exact problem for the last few versions of calibre and stanza.
Currently I am running Calibre 0.6.45 on 64bit Ubuntu 9.10 installed via the binary install python instructions listed on the calibre site.
Stanza 2.1.1 is running on my iphone 3G.
The laptop running Calibre is not firewalled in any way and both devices are connected via a wifi AP.
Within the "Computers Sharing Books" section of the "Get Books" screen in Stanza, it lists calibre running on my laptop.
Upon clicking it, stanza attempts to connect for 60 seconds before timing out.
If I manually add it as a source as
http://192.168.1.4:8080 it works perfectly.
Here's something interesting from the log:
[27/Mar/2010:15:51:35] Failed to start BonJour:
[27/Mar/2010:15:51:35] Traceback (most recent call last):
File "/home/kovid/build/calibre/src/calibre/library/server.py", line 423, in start
File "/home/kovid/build/calibre/src/calibre/utils/mdns.py", line 75, in publish
File "/home/kovid/build/calibre/src/calibre/utils/Zeroconf.py", line 1345, in registerService
File "/home/kovid/build/calibre/src/calibre/utils/Zeroconf.py", line 1432, in checkService
NonUniqueNameException
If I didn't know better, I would assume that Kovid has hard coded some calls to various core scripts?