My recent (3/5/12) experience with iBooks and Calibre server (0.8.41) is quite different. My server is at:
http://grumpy.gcsu.edu:8080. I'm using an iPad 2 with the latest OS (5.0.1) and latest version of iBooks (2.0). Here's what I am experiencing:
1) Using the address
http://grumpy.gcsu.edu:8080/ I get the same web UI as on the desktop. Tapping on Newest, I see a listing of 47 eBooks, however, there is no way to initiate a download and thereby invoke the "Open in iBooks" dialog. There is no redirect to the mobile UI.
2) Using the address
http://grumpy.gcsu.edu:8080/mobile, I get the mobile UI with the epub buttons as described. However, when I tap any of those buttons, I get a 404 Not Found and the error message: book: 360 does not have format: EPUB. Looking at the same book in Calibre, I confirm that it is, in fact, and EPUB file and that there are no other versions of the book in another format. There is only one.
3) Using the address
http://grumpy.gcsu.edu:8080/opds, I am redirected to reader.mac.com/mobile/v1/http%3A%2F%2Fgrumpy.gcsu.edu%3A808052opds. Tapping on Newest, I get a .Mac Reader Error as follows: Server Not Responding.
With Stanza at EOL and the Lexcycle web site unavailable, this is becoming a more important issue. Can anyone else reproduce my experience or, better yet, figure out what I am doing wrong on my end?