Ok, it seems that my problem is because I setup the main blog in the http://sitename.net format, and Wordpress (apparently) only works (or works best??) if sites are all setup using the http://blogname.sitename.net format.
I guess if I want sites that use top-level (rather than sub-) domain names, then I MUST use one the domain/site mapping/managing tools/plugins to accomplish that, and can't set up any sites that way directly withing WPMU?
This is a bit confusing since I'm using a virtual host in Apache to host this installation - with the FQDN (i.e. sitenname.net) I used when installing WPMU. I figured that wouldn't be an issue, at least for the primary site.
Ultimately our goal is to have some sites that use unique top-level domain names, and others that use subdomains - often of other servers/sites (using A and/or CNAME entries).
The odd thing is, the site itself never had an issue. It was only when I was in backend that it was apparent that something was seriously wrong.
Reading through the comments/suggestions, I decided to just try creating a new blog, named test.sitename.net, and it's running quick and zippy, with no apparent issues (so far).
This is after I got a dump by rerunning Site Admin -> Upgrade, and got the following (yes, my actual site URL is replaced):
Upgrade Site
* http://sitename.net/
object(WP_Error)#154 (2) { ["errors"]=> array(1) { ["http_request_failed"]=> array(1) { [0]=> string(24) "couldn't connect to host" } } ["error_data"]=> array(0) { } }
Warning! Problem upgrading http://sitename.net/. Your server may not be able to connect to blogs running on it.
Error message: couldn't connect to host
I'll install the multisite and domain mapping plugins and see if I can figure out how to correctly use them to acheive our desired results.
Now I have one more question - how do (or can) I reset/rename the original site so that it's topblogname.sitename.net rather than sitename.net? (note: I just tried Edit Blog in the list of Blogs to change it blog.sitename.net, and that only caused an infinite loop error in Firefox)
Thanks for all the help!