So I have the latest version of Hekili (just updated today, 4/2/2020).
My problem is with the Primary Display.
I have 2 icons selected, the main (I guess Primary) icon is sized with the w/h adjustments and it works fine but the second icon is not sized the same way, its smaller! I don't know how I adjusted the 2nd icon to be smaller (I do remember doing it) but I don't remember how I did it.

So, somehow the second icon and if I add a 3rd or 4th, they are all the small size and not the size of the "Primary" icon.

/hekili > Displays > Primary

You start on the Main tab, where you can see Width and Height for the Primary Icon:

At the upper right, change Main to Queue. This is where you adjust the height of queued icons.