You could be swapping. If you're running on linux, figure out the PID of your 3dMVM process, then follow it to its child R process (3dMVM itself is a tcsh script that calls R, so it won't be using much memory itself). I'd use pidof or pstree for this, though you can do it with just ps. Then you can `grep VmSwap /proc/$pid/status` and see if your R process is using a lot of swap space. I don't have all that much experience with what to *do* with that number, but I'd imagine if it's small, then memory isn't your problem; if it's large, this *might* be the problem.
ijs