I've confirmed in Studio that I have a server.database.path set to a good directory when running server.sh. But when I create a database (with studio or console "create database ..." command) it always appears in the orientdb-home/databases directory.
A short analysis of this problem, which I also noticed in 1.6.0 and 1.6.1-SNAPSHOT (as checked out today from 1.6.1-hotfix branch)
OServerConfiguration.getStoragePath(..) should honor the server.database.path setting. Instead, it returns null, which leads OBinaryNetworkProtocolAbstract.getDatabaseInstance(..) to set the default path (i.e. orientdb-home/databases).
Thanks for the bug tracking, I moved it in 1.6.1.
Fixed issue #1235
The fix works. At first It seemed not to, but that was due to a directory access rights issue.