I've got a similar problem. After Upgrading from 10.3.1 to 10.4.1 the layout of my models is corrupt. The shapes of all tools changed to a layout similar to picture 2.tif. If I change 'Shape' in the 'Selected Node Properties' to something different and then back to 'Rounded Rectangle' everything works out fine. But I don't want to do this for every tool in every model I build so far. 😞
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