Buttons size change when clicking 'Publish'

Hello,
I have a 2 sets of buttons (one on top of the other) + bookmarks so that a user can easily navigate between the views. Buttons have the same properties (differences: buttons in the top layer have different color then the bootom one, also one of the layers have 'on hoover' color change).

I've manually adjusted the position of buttons so that horizontal/vertical values are the same for pair of buttons. So everything is perfectly aligned - if i make top button transparent it is 100% aligned to bottom button.

Now the problem is that when i hit 'publish' then dimensions of some of the buttons change by 1 point/pixel... Or they move 1 pixel in random direction.

Is it a known issue? Is there any solution for that now?