Thanks for the response.
I did make sure that there is no speedplay base plate bolt sticking out of nut. Also is it necessary to cover the nut inside the shoe? Upon observation, it is indeed that the original bont insole is very thin compared with my lake shoe. Moving my lake shoe insole into my bont seems to help. I purchased specialized blue insole today to see if it helps to alleviate the problem.
I immediatly ditched my original Bont insoles, and used my Specialiuzed (red) ones instead, and evrything was super after. I had to cut a small portion of the Spesh soles to fit the Bont ones.
I switched my soles with Pearl izumi Pro 1:1 soles this year. Very nice and comfy, close to the Spesh BG reds.
I'm in my 3rd year with my A-1's, and I really like them now. I got used to how to adjust the fastening.
At first, I was tightening them too much, like a "usual" shoe, and got numb feet. When I loossened them, my feet moved a little too much (1-2 mm is too much) and hit the carbon "tub walls", and it was worst. Now I tighten them just enough so my feet don't "rock", and I can ride for hours without problems.