I'm still pretty new to Godot and I'm not sure why this is happening. Myself and one other play tested it and didn't experience that. But then he did later. Might have to do with different resolutions? Thanks for playing!
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Hey, I tried it again and found the problem. I had my screen running at 60Hz and when I switched it to 144Hz the boxes were properly spaced and moved faster.
I guess you are moving the boxes in function _process(delta), right? The best solution would be to always multiply the distance the boxes move by the 'delta' argument and a speed multiplier.
Good luck on your Godot journey!