We are using Flex to develope flash tool, we have issues when embedded in iframe, if we are using default window wmode, everything is working fine, but unfortunately we can't use this mode because the iframe has a dropdown list and has to be above our flash layer, so we use opaque mode, we find that there are following two major issues:
1. UI rendering is messed up when user scrolls up and down using the scroll bar
2. user can't type in non-ascii characters
I have definitely experienced the same issue(s). I was able to overcome these issues by upgrading to a later version of the Flex SDK and wrapping all of my content in the appropriate control for scrolling, eg when scrolling spark components, wrap them in a Group.
There are a lot of weird bugs with Flash Player when using wmode:opaque. I can't scroll using my mouse wheel when using wmode:opaque, and weird things happen with text inputs. This is a major bug in Flash Player that really needs to be addressed.