It is quite simple. PayPal will not release the funds to you until it has the funds itself - this is usually very quick as you have already discovered.
eCheques are used when the instant payment has failed - usually because there is no valid credit card on the buyer's PayPal account, perhaps because it has expired or been cancelled.
So now PayPal has to request the money from the buyer's current account (no automatic payment authority set up) and wait for the funds to arrive.
There is one big advantage to eCheques, particularly if it concerns a large sum. There can never be a chargeback as can happen with credit card funded payments.
Once the money is in your account, you can be certain it will never be claimed back.
If the buyer were to send you a cheque, he would have 7 days to post it, then you would have to either go to the bank or post it to your bank, then wait. So eCheques are still more convenient than cheques.