What have you got in your startup.fil?
I have a fairly large startup.fil (for 2 axis lathe) because I've included my homing routines within it. However, these are my first few lines, and I cannot even recall why I put them in, as they command native Galil commands to accomplish something But if you do some research on them, maybe you will figure out why they are in there, and how to modify them for your usage. I have not had any problems with startup motor jumps or anything like that.
COMMAND OE 1,1,0
COMMAND VT 0.8,0.8
COMMAND IT 0.8,0.8