WP Super Cache not allowing ads to rotate/refresh

That’s the whole point of WP Super Cache, isn’t it? To make your site static.
W3 Total Cache has basic compatibility with AdRotate.

Arnan, in a technical sense you are correct, but in reality the display and rotating of ads should be independent of any caching (or we should at least have that option). Caching the ads not only skews the impressions, but advertisers aren’t getting their monies worth. There must be a way to exempt Ad Rotate from WP Super Cache.

If it can be done during the page generation, then perhaps Ad Rotate can take an ajax service approach. An ajax service page can return ads from a service page that is marked as non-cached. Not sure if that’s possible, but it seems like a logical solution.

Enabling the checkbox and clearing the cache works just fine.
You can enable caching support in AdRotate settings.

Yes a jQuery function would be nice, but I haven’t found a good way to do it yet since Javascript can’t talk to MySQL and AdRotate needs it’s database.
Having JS load a sort of iFrame which talks to MySQL would be too taxing for your server. Too many connections etc.

If you really really need caching because your site is slow, consider getting better hosting.