Hello Ken,
Sorry for the late answer on this.
The On-The-Fly view is supposed to display only issues of the currently opened and focused file. I wonder what was happening in previous versions, maybe MyEclipse (which I’m not familiar with) behaves a bit differently ?
This behaviour is by design. With our products we want to encourage people to clean as they code, so we help them focus only on the relevant information.
We’ve had several similar requests in the past on this forum. As of today it’s still not part of our roadmap to add filtering on those views