I got it to work like this:
On the Advanced tab in WP Supercache:
1. Switch to PHP to serve cache files.
2. Click Update Status.
3. Switch back to mod-rewrite.
4. Click Enable Dynamic Caching.
5. Click Update Status.
6. Go to Contents tab.
7. Click the Delete Expired Button and the Delete Cache button.
This is all happening because the WP Super Cache update turned off dynamic caching, and Ad Injection won't work.