How large is the file you want to scp and where is is located on the cores? I'm trying to reproduce your issue, but I may not be understanding it properly.
I went on marc005 (one of the systems assigned to Intel) and tried copying mkl.tar (about 260MB) to /root on rck00 and ran out of space. So I then tried a small file as a test. Is the following what you are trying to do for larger files?
root@rck00:~> cp /shared/tkubaska/hello.c .
tekubasx@marc005:~$ ls -l hello.c
-rw-r--r-- 1 tekubasx admin 69 2010-12-05 11:30 hello.c
tekubasx@marc005:~$ cat hello.c
Note that /shared is a a directory on your MCPC that is mounted on the cores. If your core program writes to /shared, the data are already on the MCPC, but I suspect you already know this. You probably want to move the data to your /home on the MCPC. Is it not acceptable to write to /shared on the MCPC and then copy to your /home?
We do have an example of how a program on a core can run a script on the MCPC, if that's useful. Look in "How to Read SCC Voltages with a RCCE Program."