Well I don't run CMMOS on 2000, however it seems odd that it's looking for the log file within the executable. Take a look at the log file in your CMMOS directory and at the top it has the installation directories for CMBO and CMMOS. Below is what I have.
CMMOS install folder is C:\Program Files\CMBO\CM Mod Option Selector\
CM:BO install folder is C:\Program Files\CMBO\
I had problems with the previous version when I installed CMMOS on a secondary partition, is it installed on your c drive?