Hi Kaushik,
Here are a couple of additional things I would do on the same lines as Dave suggested to resolve it.
1. Can you check the logs for the commodity codes upload within GTS? If there are no errors, it would mean your GTS system doesn't have an issue as all the files carrying the relevant UoM and supplementary units are loaded successfully.
2. As Dave rightly suggested, verify the T604 or use CUNI transaction and verify the relevant UoM exists in ECC (use the internal measurement unit column value from table /SAPSLL/TCOTSU when you are trying to check in T604 and not the supplementary unit by itself)
Hope it helps!
-Shrini