I think we need some more information to be able to help you. It sounds to me like it's your host computer that's running out of memory, not your RT module. Is this correct? IF that's so, I'd need some details about what the VI is that you're calling by reference and whether you're calling it on the server or host. Running out of memory on an FP-2000 is no great feat; doing so on your winbox takes a bit more work.
What OS are you running, version of LabVIEW (6i, 6.02, 6.1_, etc?