There is a better way of writing it. Present Progressive has several usages, including:
1) to describe an action starting in the past and continuing to this time.
e.g. "I'm busy right now. I'm doing my homework."
e.g. "I'm reading a great book."
2) to describe a future arrangement
e.g. "I'm having lunch with the chairman this afternoon."
3) It can be used with if, and while in dependent clauses for a future reference.
e.g. "If he's sleeping when you get there, wake him up."
What you are describing sounds like a pesky pop-up that continually reappears whenever you try to complete a payment.
Habitual actions are best described using simple present tense.
So, your sentence would be better written:
"Everytime I press the check out button, the pop-up "Our site is not set up to accept internet payment" appears.