Taxation of capital gain out of equity

I had ESOPs of an private limited company. (in around 2001)

after a pretty long time, the company got taken over some foreign company.

Now, due to this I had to sell all shares 2013-2014, and i got a handsome profit out of it.

The amount of profit was such that I cannot pay tax on it. And I decided to invest in a residential property.

Now, I already own a residential property and have one housing loan running on it.

I calculated the indexed cost of my purchase and deducted from my sell value to get the capital gain. I invested this in the Capital Gain Tax Savings Scheme to park the fund for finding the resindential property.

Now, while filing return, my honourable CA has considered following, which I think is incorrect.

1. Since I have one property, I cannot get the benefit of this scheme/section

2. according to me, I should have invested the net sell value (capital gain amount) and I have invested the same, but my honourable CA guides me that I need to invest the full sell value (without deducting the indexed purchase cost)

I am looking for your genuine guidance on the matter.

Thanks