User Environment variables overriden by system env variables

Hi,

I've got several env vars defined for me as a user,
and also defined as part of the System env vars.
when I open a command shell, I only get the values from
the system set. In particular, the PATH user variable
is not concatenated or prepended to the system PATH
variable and so some applications cannot be run from
the command shell.

Any idea how this is supposed to be done - I may have
not set some property or such to allow this to take
place...

Any help will be greatly appreciated