Speeds up website but messes up images and ads

I agree that this is probably the best free cache plugin. It improved one of my websites fully loaded time from 6 seconds to 3 seconds and requests from 105 to 46. But this was with scripts merged. However, this was affecting ads –they were not showing, yet my website depends on ad revenue — and images, which were also not showing. Once I unchecked “merge scripts” the website functioned normally again. However I went back to over 100 requests and a fully loaded time of 7.8 seconds. Question is, how does one merge scripts without breaking useful functionality?