I am having a similar problem since switching to 5.4. I have to add multiple toolbars using window_load_component_file and in 5.2 they would nicely stack vertically. I did not change the code to add them at all but in 5.4, they are being added at the horizontal end of a row even when there is not room for them and I can't get them to stack nicely. I will try to follow the good numerical code used earlier.
and half of Toolbar 2 is cut off.
I didn't know that you could specify x,y coordinates for toolbars, now that I have done so things look much better. Thanks for the tip! Version 5.4 must handle unspecified coordinates differently. My code for the window adding was (and still is):