Here's my situation. For various reasons, we needed to set up a strange sort of network for a large organization with indvidual state-by-state multisite installations under a master domain... i.e....
There is a multi-site installation at: http://www.mydomain.org and then there are separate multi-site networks installed in each US state subdirectory... i.e. http://www.mydomain.org/nc/, http://www.mydomain.org/ny/ etc.
So I installed the domain mapping plugin on the master domain an it works just fine. i.e. northcarolina.org maps correctly to http://www.mydomain.org/northcarolina
Where I'm having a problem is getting the domain mapping to work on the subdirectory installations. For example: I want to map the domain ncsite1.org to http://www.mydomain.org/nc/site1
When I go into site1 and select domain mapping, the original blog address http://www.mydomain.org/nc/site1 shows correctly, but when I put ncsite1.org into the custom domain and click add...the resulting custom domain comes up as ncsite1.org/nc/
Naturally, I get a 404 Not Found error from the Apache server.
Am I doing something wrong or is there any way to correct/workaround this? I'd really like to offer the domain mapping to the users at the state level.