Ok so guys, I have an update. After failing with many attempts including an attempt from a US based credit card from within the US. I contacted the apple support through their contact page. summarized the problems listed all the Apple IDs i had tried and gave all the case numbers as well.
The nice lady from developor support messaged me to setup a time for a call - we did one call and setup another call. I created a new ID and had a card ready which was never used but i did not proceed the payment. She called me and took my card details and she did the process at her end. 2 days later i get the confirmation from my bank and apple that payment has been done. I got the developer program confirmation email as well. Now the account is enrolled.
The lady was really helpful and she called and emailed at the exact time we agreed on.
There is definetely something wrong with Apple's system but the last support i got made it.
I suggest you also do a detailed summary with reference numbers and contact apple support and maybe via wire transfer or by phone your account goes through too.