Your design shows a 6190 ohm resistor for R8. Did the design software specify this value? This is too large a value for the TL431 to properly control the output voltage. Something like a 470 ohm resistor would be more appropriate.

yes 6190 ohms was specified by the software even i was confused about that.
Can it be a problem of "no load" i have read it somewhere to maintain the regulation, a minimum load has to be applied to one of more of the multiple outputs of the supply. Can u also specify what RTN is? Is RTN the negative terminal and is it different then GND1.

Thanks alot for your reply .I have replaced resistor R8 6190 ohms with 470 ohms resistor as you mentioned. It made the output voltage 12V constant at one output but the other output shows 21 V on no load and when i connect my LCD Screen with operating voltage (5- 30v) it just drops the voltage to something like 10V - 15V .kindly let me know what could be the problem or is it suppose to show 21v on no load. Why that output is not showing constant 12V. Schematic attached

First thing - it it necessary for your design to have two outputs with separate grounds? This is the worst case for output cross regulation It sounds like you might be able to use a single output supply.

If you absolutely need to have two isolated outputs, there are some steps that can be taken to improve regulation on the second output. First, though, I need to ask a couple of questions -

1) When you loaded the 2nd 12V output with your LCD screen, what was the load on the regulated 12V output?
2) What is the required load range for the two outputs?
3) Did you design and build the transformer? Please include design files if you have them.

Adding a preload to the unregulated 12V output will help keep the output voltage from rising too high when it is lightly loaded. You may need a preload on your regulated output as well if you have a situation where the regulated output is lightly loaded, and the unregulated output is heavily loaded.

The schematic shows ground and return because you have 2 outputs with separate grounds. This may not be necessary for your application. If the LCD screen and the load currently on your 12V regulated output can share grounds, you can use a single 12V output, and you will have far fewer regulation problems

1. The load on the regulated 12 V output was my microcontroller which takes about 800mAmps
2. the required output is 12V 2 Amp for this purpose i require two isolated outputs 12V 1amps each to power my microcontroller and LCD screen from same power supply.
3.I did not designed and build the transformer by myself the power integration software provided me with transformer construction document for my design that is what i provided to the manufacturer and get it done.
I am attaching both documents * Transformer construction Document and the one the manufacturer provided me with

I still don't quite understand why you need two separate grounding systems for your LCD and microprocessor. Perhaps you can explain more about your system design.
. Also, the transformer is not set up for optimal efficiency or regulation. The primary should be sandwich wound instead of single section to reduce leakage. Also, if you care about cross regulation in the two secondaries, they should be wound bifilar on a single layer, which will increase coupling and improve cross regulation.
If you can possibly run your microprocessor and LCD with a common ground, you can solve your regulation problem.