Are you sure you have a file called startup-sequence in the s: directory of your bootable partition? The first line of startup-sequence should be c:setpatch. Maybe you are also having a problem with the rom updates of 3.9? You could try commenting out the rom update with the command SKIPROMUPDATES (or something similar) after the setpatch command. There are instructions on how to do this on the 3.9 cd.
Edit: ah yes, do as Thomas suggests, a smaller bootable partition.
