In Budget 2016, clarity was expected on the long term capital gains in the hands of the owners in JDAs but unfortunately this was not done. There are conflicting judicial decisions on this issue. As most of the owners are individuals and unorganized, most of the JDAs are drafted to the advantage of the Developers, with absolute rights granted under GPAs, thus invoking the incidence of capital gains in the hands of the owners the moment the agreement is signed.
The agreements with the builder need to be studied in detail to determine the time at which the transfer takes place. Presently I am also dealing with similar case. You may contact me if necessary.