MEB 7.5 Websphere for Developers 6.1 – deploy problem

I have Websphere for Developers 6.1 installed locally. When I deploy my application to the server outside of MEB then everything works fine. During the start up custom system variables are read e.g.

System.getProperty("my.variable")

. The application is dependent on these custom properties.
They have been set via the admin console:

Application servers > server1 > Process Definition > Java Virtual Machine > Custom Properties

However when I use Websphere within MEB and start the server up, these properties are missing when the class tries to read them. If I go into the admin console (still in MEB), I can see that the custom properties are set OK.

What’s going wrong? I must be using the same instance as 1) I can see the properties in the admin console and 2) JDBC resources are resolved OK.

The same happens if I try to deploy the EAR project rather then the EAR file.