I've had a very similar problem, specifically with a Sales Order.  For reference this is on Enterprise 2023.  The template layout was working just fine, spacing, sequence, custom columns included.  Layout designer, preview and print all matched accurately.  Then I tried to make a revision, trying to add a column to accommodate some need here.  That change seems to have thrown everything off.  Layout designer saved the layout as I had created it, correct column widths and sequence, but print preview and printing revert to something different.  As usual all of the boiler plate suggestions by QB staffers did nothing.  The solution that seems to have worked is to uncheck the Backorder column.  I don't actually even recall why I was trying to include this on a sales order, but it seems that is the conflict.  Including the backorder column seems to override, or perhaps conflict logically, with other settings and throw everything off.  Uncheck it and we're back to normal.  I hope this helps others having the same problem.