Do you have strict site isolation enabled in chrome://flags? We’ve heard reports of this causing exactly this issue. If you’re willing, try reseting your flags to their default values and see if that fixes the problem.
Edit: Specifically, this known issue in Chrome:
In some cases, clicking or scrolling on cross-site iframes may not work properly.
For example, this can happen when there is a partly transparent overlay above an iframe. (This is fixed in Chrome 65.)