Here is an option. A site that I just completed is using ads from commission junction. The owner of the site is able to go through commission junction and choose the ads he wishes to see on his page then download the code.
I created a table in the sites db and we enter the html for those ads into the db. I then can randomly call ads from the db and keep track of the clicks by adding a field that acts as a counter.
If you are able to choose the ads and download the code for them with the ad provider you are with, this will work fine. Otherwise, I agree that it sounds like an javascript issue.
Later on and hope that helps,
Terrence