I think this anomaly will get fixed soon. Trades done on MCX, NCDEX is considered as non-speculative business income. This means that if you make any loss, you can set it off against other business income. So for example if you had a trading loss, you can set it off against bank deposit returns, rental income, etc. But if it is considered as a speculative business income, you can set speculative loss only against speculative gains.
You can check more on taxation when trading here.
There is hardly / nil volume of commodity in the nse !