this is correct, the applications started by your startup folder will be run under the same account as the one who has logged in.

if you want to start an application with full rights, you could create a service which can do that.
for this you can use instsrv.exe which can be downloaded for free from microsoft since it is a part of the resource kit.

usage:
instsrv.exe <name of service> <path to executable>

example:
instsrv.exe MyService c:\test.exe

there is only one thing: not every program can be started as a service like this.