PayPal IPNs are how we know an order has been placed, so if yours were disabled that would explain the problem and you fixed it correctly.
Typically IPNs are enabled by default. It's not necessary to enter any special notification URL for PayPal to send the IPN to with our system because we provide that information to PayPal ourselves. However, if your IPNs have been previously disabled for any reason PayPal won't send anything back to us regardless of what we send to them.
One catch about enabling IPNs in PayPal once they were previously disabled is that they will require a Notification URL to be entered in order to turn IPNs back on. Our URL
https://www.e-junkie.com/ecom/ipnext.php can be entered for that purpose, but any URL that can accept IPNs will work just fine there. That does mean you can have your PayPal account send IPNs somewhere else for purposes outside of your E-junkie cart, it will not interfere with our process at all to use a different Notification URL.
As for using the same PayPal account for two different E-junkie accounts we will not have a problem with that either as long as you are using two different emails with that same PayPal account. We will determine which of your E-junkie accounts is involved with an order based on the PayPal email you enter into each E-junkie profile. It's not even possible to use the same email in two different places there, so you are in no danger of getting your orders mixed up between your accounts.