Thanks for checking in; I was worried I was alone.
Out of curiousitiy, did you try to install Fink or MacPorts before you realized this problem? I would be interested to know if there was a causal connection with something I was working on.
I have two macs in my place. I installed the server app on a MacAir running Mountain Lion and verified that it wasn't having the same issue. In spite of all the negative reviews of Mountain Lion (especially the process of updating the server app), I went ahead and updated my Lion MacMini Server (where I was seeing the error) to Mountain Lion server. The process was relatively straight-forward, though I recall being mildly scared of data loss at one point. Now everything is fine.
So - I know of no "solution" per se, but I can verify that the problem does not persist across upgrades.
Hope this helps.