If you're working on the Tresidder machines, you have 16MB of memory
but applications only request a certain amount when starting up. The
default allocation for the kernel is 5000K and for the front end
1500K. You might try (1) quitting out of other applications and (2)
then setting the "Preferred Size" to 8000K for the kernel, 3000K for
the front end. This should give Mathematica a lot more space to play
around with and prevent at least some of the problems you're having.
As always, save often. :)
- john