Several people have experienced difficulty when moving the MkLinux control panels
and extensions from one system folder to a system folder on another drive:  
MkLinux refuses to boot up from the second Mac system folder.  

First make sure that you have a lilo.conf file on your desired startup disk, and
make sure that it is correct.  lilo.conf is located at the following path:
Your-Mac-Startup-Drive:System Folder:Preferences:lilo.conf

Its contents should look something like:

# 'rootdev' defines the location of the root device.
# This is the only supported option (at the moment).
#
rootdev=/dev/sde3

If that does work, you may be forced to reinstall MkLinux to get it to 
boot up with the other Mac system folder (This time when you install, make 
sure you boot off the correct Mac system.)