I will probably not be of much help with your problem as I'm not at all familiar with Clkinout.exe but...
Example: if I run the batch from My Document folder on my workstation it will look in My Documents for the SC directory instead of on the S:\ drive. Even though the executable is running from the S:\ drive.
The OS default drive is not affected by where you run the executable from and will remain as C: or C:\My Documents etc.. Seems to me that the S switch in Clkinout.exe is not working or its format is wrong.
Can you change the OS default to S: without affecting the operation? Such as your bat file could be:
S:
CD MITC2000\T-TRACS
CLKINOUT.EXE S "SC"
The default is now S:\MITC2000\T-TRACS and the .exe is run from there.
After program execution the default could be changed back to whatever using another CD command if required.
In the shortcut currently used START IN: S:\MITC2000\T-TRACS does the same job as the CD command shown in the proposed file.