Just read this comment from a user named Chandan Kumar and you’ll understand the problem. It’s not just him; the problem occurs for a good 10% of transactions that take place through IRCTC’s current payment gateways. 
You patiently enter all the passenger details, select your payment option, go to your bank’s website and authorize payment and unfortunately, it all ends there. It doesn’t redirect back to IRCTC website at all (or doesn’t redirect in time); which is needed to confirm your booking. Even worse, your bank debits money but your tickets are not confirmed by IRCTC. All you can do is start from the beginning. And just imagine if this occurs while booking a tatkal ticket; you can rest assure that the few remaining tickets will be already booked while you go through the process once again.
It’s just, TERRIBLE.
So how do you solve the problem?
Simple; remove the need to go external websites to make the payment.
That’s what IRCTC will do soon. It will introduce something called as ‘Rolling Deposit Scheme (RDS)’, commonly known as e-wallet. You prepay (or top-up) your IRCTC account with (sufficient) money so that you can use this account to pay for your tickets without ever leaving the IRCTC website. The transaction time is significantly reduced and there are also no service charges, often levied by the banks’ or payment gateways.
You can top-up your IRCTC account with a minimum amount of Rs.1500. Unused amount will keep rolling over. We are informed that the registration fee for RDS is Rs.250, which can be redeemed while making your first booking.
Tip: It makes sense (especially if you are booking a tatkal ticket) that you top-up your RDS account well ahead of the planned booking, since you will still have to visit your banks’ site to add money to RDS account.