Before we go any further, I want to ask a question that is so obvious you might find it insulting, but I honestly mean no disrespect. I would be irresponsible not to ask. When you kick the engine over, are you absolutely sure that the engine is is at TDC on the compression stroke every time? I ask because what you describe sounds like you are checking or setting the valves sometimes at TDC on the compression stroke, and sometimes at TDC on the exhaust stroke.
Now that the cover is off, it should be very straightforward to see what the problem is. But first of all, align the dots as you have in your second photo, and then adjust the valve clearances. Next, kick the engine over a couple of times and then ease it forwards until the marks all align again. Then check the clearances again. Repeat a couple more times.
If the clearances genuinely do change, even when the dots are aligned, then you need to diagnose further.
The mechanism is fundamentally simple. Put it to TDC on the compression stroke, then check each stage of the mechanism:
* timing marks all correctly aligned
* cam followers resting on the base circles of the cams
* push rods sitting firmly and squarely in the cam followers
* tops of the push rods sitting firmly and squarely in the rocker arms
* rocker arms firmly bolted down to the head
* a small clearance between the rocker arm tips and the valve stems
* see if you can arrange some sort of lever to push down on the valves so you can see if either valve is sticking
If you are satisfied everything is correct, then kick the engine over a few times, ease it forward until the dots align, and then - if the valves are extra loose or extra tight - do that sequence of checks again.
As I say, it is a fundamentally simple mechanism and I am certain that you will be able to see the fault by close and careful inspection. Some of it is tricky and you might need a torch to check that the followers are sitting on the cam base circles, but you can definitely do it.