I think its your LEFT /RIGHT axis that needs to be adjusted.  I borrowed your photo and will photochop it and repost.

I am going to make some pan head assumptions here.  It appears that your camera might be a dSLR and that you are using a fisheye lens and you might be using an Agnos Mrotator TCPshort pan head.  IF so.. then your right left parallax removal dimensions might be off by 4 to 8mm.  I measured the Allen screw head and it is 8mm diameter.  The black void box in your photo is about 8mm square.

Write down your current Left/ Right  scale measurement lets say its 42.

You need to slide the L bracket either 1/2 the distance or 4mm  left or right .. not sure.  Say 38. (42-4=38) Then retake a pano and do another screen shot of the nadir area. 

If the black box got larger.. then redo 4mm on the other side of 42 mark or now 46. And do another screen shot of the nadir.

With a Canon 5d/ Sigma 8 and Mrotator TCPshort here is what mine looks like:

Well 36 is getting real close.  You might also try 35.5 and 36.5.  My fingers are too large to measure any thing smaller than 1/2mm.. Argggg.

So how did the 36 mark panorama look.. along the seams???

I did have some experience with this.  I moved my camera all the way over to the 0 zero mark and shot, stitched and screen captured 
a pano  at 0, 10, 20, 30, 40, 50, 60, 70,  and I skipped 80.  I think you are down to the 1/2mm mark now for yours.

Possibly the reason you are seeing different shaped screws is because your camera might be TILTED up just a very tiny bit. 
But that is extreme observation.  As long as the image seams are coming together quite well.. blending should take care of it.

By the way if you could resize your images down to 600 pixels wide it would help.

Dave

I think you found the L/R parallax fix at 36.5.  Knowing where those screws are located and seeing them in the photo... forward/backward
 that tripod rotation center point is right on the mark. I would leave it as it is for the moment.

How did the 36.5 mark turn out along the seams?

Dave

Looks like your still  1/2 mm off.  However, What works.. works well.  Job well done.  YOU did all the work

All we did was to point you in the right direction.