Here is the most likely cause:
The domain root of the server running (I assume at 4848) is different than the domain root of the server that asadmin thinks you are trying to stop...
here is a for instance that may clarify the situation for you.
Say you have installed the app server in /a/b/gfv211 you started /a/b/gfv211/domain/domain1 and it is running on port 4848.
In a different window, you call asadmin stop-domain domain1. In this window, asadmin resolves to something like /c/d/gfv211/bin/asadmin. The stop-domain command checks to make sure that it is going to stop the domain installed at /c/d/gfv211/domains/domain1...
Since that isn't the domain that is running on port 4848... the command exits with an error message that says that domain1 is not running. I filed
https://glassfish.dev.java.net/issues/show_bug.cgi?id=12783 to track this
vbk
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