I’m currently updating my homepage with layout blocks and perhaps two of my own experiences while working with them might be helpful:
One good thing in sparkle is the independence of size and position of items in different layouts. But this also may cause a problem: Let’s say, you want to create three identical boxes using them as backgrounds. You create one and then you copy and paste the two others. Now you arrange them on your landscape page: box 1 at the top, box 2 in the middle and box 3 at the end. When creating the portrait smartphone page, it might be possible that you arrange them in a different way, simply because you selected box 3 first and placed this box at the top, box 2 in the middle and box 1 at the bottom. Normally it doesn’t matter because the boxes are just identical.
But when you use layout blocks and you select box 1 (top) on the landscape page you select exactly box 1 in portrait Smartphone layout, which, in my example, is placed at the bottom of the page.
And now the confusion is perfect: In landscape mode all seems in the right order while in portrait mode the items are grouped to a layout block widely scattered over the page.
You can avoid this by the use of a strictly identical sequence of the elements on all layouts, which is no problem when creating new sites but might be a slumbering problem in existing projects especially when revised several times.
That might be the reason for your problem.
If you collect some elements by selecting them while pressing the “Shift” key and you want to arrange them to a layout block, the sequence you select the items is reversed arranged in the layout block. For example: to arrange a text box over a background box you have to select the background first and then the text box. In the layout block they are arranged properly.