Shnuddy, I am inclined to agree with Yuki that there might be one more nuance with the imperfective. "Открывать окна" CAN imply long expectation of a permission.

Imagine another situation:
You are going to visit your friend. You approach his house and knock at the door. But your friends want to make a surprise for you, and he asks you to wait a little:

- Подожди, не входи.

After you wait for a while, he finally says:

- Всё, можешь входить.