It's ok to manually fill the cap top with a syringe and cleaning solution if you need to get it done quick. As for the reason it's not filling, you might have an air lock in the tube. The solution isn't pumped and just uses gravity to fill the cap so if there is an air bubble in there, it can stop the flow. Open the valve and pull some solution through the tube to see if you can get the air out of it. Also, make sure the valve is opening and closing properly.