Ducts can "look" sealed, but until you test them for leakage, there is not a consistent way to verify how tight they are via eyeballing.
90° elbows, such as shown in your photo of the return with the filter removed, are notorious for leaking around all of those "ribs" you see on that elbow. Seldom are they sealed during installation; if any sealing on ductwork is done at all it is typically where the flex connects to collars, elbows, plenums, etc. Which is good when they do that, of course. But if the elbow joints (ribs) are not also sealed, you can well be pulling attic air into the return ducting and distributing same, unfiltered, through the entire house.
Two questions about your house, if I may:
- Are there pull-down stairs to the attic inside the house? If so, is there any weatherstripping where the hatch meets the ceiling?
- Do you have any recessed light fixtures in the ceiling that penetrate into the attic? When you are in the attic, can you see light (given the fixture is not illuminated and any attic light is also off) entering the attic from the house below through the fixtures (provided they are not buried in insulation)?
I mention these two items (which are only two among several related matters) that could be contributing to your health problems. The overall idea is to get an attic as isolated from the house as possible. Many builders have not yet grasped why this is so important, as in spite of technological advances, we keep building houses very similar to how they were made fifty years ago. Only styling and size has changed, with perhaps modest technical gains and technique changes in construction, such as better windows, composite materials, etc.