What I did:
Made a blog on wordpress.com that I used for a while, let's call it subdomain1.wordpress.com. Then, under that account, I made another blog at "subdomain2.wordpress.com". I tried to add subdomain2.wordpress.com to Blogilo (I don't use blogilo for subdomain1, by the way, but I've used blogilo for unrelated blogs in the past) -- I entered subdomain2.wordpress.com and my username and password into blogilo's "add blog" form and clicked "Auto-Configure", and it switched all the info to the subdomain1 info. I couldn't find any way to fix it. I even tried switching the field back to subdomain2.wordpress.com/xmlrpc.php, and also going on the Web logging into my wordpress.com and looking for the Blog ID#s to put into "advanced" (the only place I could find them was on subdomain.wordpress.com/wp-admin/index.php?page=my-blogs , mouse over a blog and over "Transfer Blog" and find the number in the "transfer=" field of the URL in the status-bar -- right-click and copy that URL)
In case it matters, subdomain1 is http://haddock2009.wordpress.com/ and subdomain2 is http://melioria.wordpress.com/
I think the issue may have something to with, on that "my-blogs" page I mentioned in passing above: on that page, the blogs have an ordering, and a radio-button that says "primary". Currently subdomain1 is labelled "primary", per default. I have no idea what these things mean, although with some persistent searching I was able to discover a few effects of the "primary blog" setting (some of which sound more like bugs than features)... http://en.forums.wordpress.com/search.php?q=primary+blog
Nevertheless, I think Blogilo is the main culprit here (unless it turns out the Wordpress API is broken and can't deal with multiple-blogs related to one login). I'm using Blogilo 1.0.1/KDE platform version 4.4.1/QT 4.6.2 on Arch Linux.
P.S. I switched subdomain2 to be "primary" as well as first in the order displayed on the "my-blogs" page. Neither of these made it possible for me to configure blogilo for subdomain2 (there was no observable difference within blogilo).
