Hi Gregg,
The SEPM console uses Java, but comes with its own built-in, pre-tuned version. It won't be using .NET or any other installations of Java that are on the server. (There are exceptions- if you are using remote console, etc etc etc)
How low on space is the SEPM-? Also: is the SEPM using a databse that is installed on the same server or on a remote server?
Final question: which exact version of SEPM are you using?