Ok, I get it. Just went over to a fren's comp and checked. The cut is in the part which connects to the motherboard. Also counted the pin at which the hole exists. Its Pin 28. This pin is used for cable select signal, as I said (Pin assignment: *www.archonmagnus.com/computing/elec/IDEpins.php).
When grounded (no hole) means the device is master. When not grounded (cut, hole) it refers to slave. The gray connector (middle one) is the slave and the black (other end) is the master. Now as per this terminology the master should haf the 28th pin grounded (connected, no hole).
My assumption is that pin 28 of the black connector is simply connected to one of the other grounds available (see the pin assignments). It needn't necessarily be connected to Pin 28. Its just ground, after all. Hence the gray (slave) connector has a hole in 28th pin while the black (master) has all connections intact and this is how it is implemented by making a hole in the 28th pin on the connector which plugs into the motherboard.
You may count the pin at which you can see the hole yourself easily and also do some tests. Put the jumper in CSEL on the HDD/Optical drive and try out different combos.
OK Now its all clear to me.
But as I have said about the problem now, it is not some other cable or so.
I just cut the cable near the hole and crimped it to the motherboard connector ( all parts are of same cable)!!! Now, my drive is kinda slow! It reads some DVDs with 12x speed ( which previously read at 16x ) and some other DVDs like that of sony's is read at 2x to 5x!!!.
One observation was that I used nero drive speed and that program was unable to change the speed of drive. I can't read dvds easiely. There is little problem with CDs.
Its a SONY DVD RW G170 A. Firmware 1.74. DVD Region code set to 5 ( no idea whoever did that !!! ).
What might be the problem?