Filing of return

You can only file returns for A.Y 12-13 & A.Y 13-14 now.. ( Return of A.Y 12-13 can be filed only till 31st March 2014, after which it would also get BELATED like your other returns)

Loss of Shares cannot be set of against Salary.

Also,

losses under other heads of income, such as business and share trading, can be carried forward only if the return is filed by the due date.

So, You cant even carry forward the losses. Only House Property Loss can be carry forwarded even if return is file or not before due date.

Extra Info:

If there is a net loss under the head "Capital Gains" for an assessment year, the same cannot be set off against any other head of income viz., Salaries, House Property, Business or Profession or other sources. It has to be separated into Short term Capital Loss (STCL) and long term capital loss (LTCL) and carried forward to next assessment year. In the next year, the STCL can be set off against any gains from transfer of any capital asset (Long term or Short term) and the LTCL can be set off against gains from transfer of long term capital asset only. Any unabsorbed loss after such set off can be further carried forward to next assessment year.

Capital loss computed in an assessment year can be carried forward for eight assessment years and set off as above.