Back in my film days I used to use the Cokin system, Not as high quality as the Lee, but quite versatile. I still have it but never use it now. It was a pain using a graduated filter when many Minolta lenses rotated when focusing and removing it from the lens was fairly time consuming. Now with internal focusing on many lenses it would not be a problem. However I now only use round filters and only those that are needed under certain conditions, like Polarizing, grads etc.
So I dug out my Cokin filters and had a look. Apart from quality I believe they are similar to Lee filters. What I noticed was that the slots that hold the filters in place have an open slot each side (or top/bottom), 25mm long that hold a curved metal spring to keep the filter from sliding out. I installed it on my A850 And noticed that when the sun was at the side it passed through that slot and left a dim reflection on the lens front element. The reflection was a semi curve similar to what you are experiencing. Yours are a bright curve plus a dimmer curve, which you may expect as it is caused by out of focus light. Could that explain part of your problem?
Lens used was A-mount 16-35mm ƒ2.8. The same lens i use for 95% of my landscape photography. The only other variable here is the addition of the LA-EA3 adapter so i can use it on the E-mount body. Possibly the problem?
An extreme wide angle lens, prone to flare, although not to the extent that you are experiencing. I can't see that it is the LA-EA3 as it does not have a mirror or anything inside that would cause a problem. Not like the LA-EA4 which has a mirror that can be knocked out of alignment.
I did take the images with the filters in place and without. Apart from the shot into the sun they show no sign of the problem/ flare. The into the sun shot flare is well controlled and very usable.
That would indicate that the problem lies with the Lee Filter system. Shooting into the sun with any lens may give flare and is not a camera problem, simply a limitation of lens design.
Ideally i would like to try my setup on another body and try the FE16-35 on my body to see if it continues or is resolved with either combination. No shops stock any higher end equipment here in Scotland though.
That is the best trouble shooting answer and if no problems with the second camera, Wex would have to provide a new replacement. Pity you live in an such an underprivileged country.
When I lived in Scotland, Glasgow had everything except possibly work!
Please keep us informed Chris.