Got a simple doubt on DIR pin. X_DIR_PIN will be high for one direction and be low for opposite direction right? My DIR pin is always high and hence my stepper is rotating in only one direction. Any reason for this?

Are you sure you measure the same pin your firmware switches? For comparison, see e.g. [reprap.org]

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Generation 7 Electronics	Teacup Firmware	RepRap DIY

Im having the issue only in X Dir pin. Others go from 0 to 4 point something when I change the direction. X Dir pin is always high. Something is wrong, I just don't know what

... check the correct pin assignment in your configuration.

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Viktor
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Did that. Re-uploaded a new firmware, installed new pronterface but still the same issue. It used to work properly only recently it is acting crazy. All other pins (X step, Ystep & dir, Zstep & dir, Estep) are working properly. Only X dir is constantly high.

Is it possible the IC (ATmega1284P) has gone bad? That is the last thing I have to try. Issue is installing a bootloader in a blank IC.

I was reading the Sanguinololu Reprap page and found this:
[reprap.org]

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Fuse Settings
The fuses for the atmel chip must be changed from the default factory settings to disable JTAG.

Symptoms of incorrect fuse settings:

X axis only moves in one direction.
Endstops do not work.

So my fuse settings may be bad. Got to spend few more $$ to buy some programmer and to get it rectified

I just received a broken Melzi and fixed it up, after replacing all the stepper drivers and adding a new 5v regulator all was good except the X dir pin (which goes directly to the micro) it seems it got burned after my friend connected the power in reverse.

So, if you have had any wiring issues, the problem may be similar to the above.... If you are running pre-installed firmware, then the chances are that the fuse settings are already correct...... as you wouldn't normally have to change this if the board has been flashed with the sangulino bootloader as supplied with the Marlin firmware.

You can try re-flashing your boot loader with an isp programmer, I used a UsbAsp programmer off ebay for less than £10, the UsbtinyIsp will give errors (but does work) and using an arduino as isp didnt work at all.

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Is it possible the IC (ATmega1284P) has gone bad?

Might be the stepper driver. Power down, pull the Pololu out, power up and measure again to find out.

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So my fuse settings may be bad.

Fuses don't change spontanuously. If it worked before, fuses are still set right.

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Generation 7 Electronics	Teacup Firmware	RepRap DIY