There's a Variations bug blighting the MOSS install I'm currently working with, which we may have figured out.
In the portal, you open Site Content and Structure and navigate to a Site Variation. In the settings for the variation, change the url of that site.
The link between that Variation and the source now breaks (or if it was the source it no longer propagates variations correctly). The icon in Manage Content and Structure changes to a site icon from a variation icon. The link cannot be re-established, even with Gary Lapointes custom STSADM command that he wrote about here http://stsadm.blogspot.com/2008/04/fix-variation-relationships-list.html
For some time we were unable to get any idea why this happened on this MOSS site, but was not reproducable on other sites. Now we know. It seems that the site in question was originally created with a blank team site template, whereupon the Publishing Feature was then activated. If you create a site using the Publishing Site template from the start, it doesn't break in the same way.
The issue is with Microsoft now, and we hope for a fix of some kind for the sites that are afflicted. The portal is sufficiently mature that a delete and re-create would be horrible.
I haven't seen any other postings about this issue, so if your site is afflicted too, try the reproduction steps I detailed above.
UPDATE 16052008 - There is a rollup of Variation fixes being released by Microsoft in a couple of weeks or so. It appears that this issue will be fixed in that release. Fantastic! Looks like Variations are about to become the robust feature we want them to be.