I’ve noticed that in Designer the “Align Objects” function sometimes doesn’t work right. The objects will be moved but not aligned correctly. It seemed to be random, but I finally figured out what is causing it. Here is source code to demonstrate (from a print section)
<p>
<br>
</p>
<div anchor="page_media_0"
style="font-size: 20pt; font-family: Arial; position: absolute; overflow: hidden; box-sizing: border-box; width: 90px; height: 30px; top: 661.467px; left: 155.067px; text-align: right; border-width: 1px; border-style: solid;" offset-x="192.86699923706055" offset-y="699.2669992370605">
<b>200265</b>
</div>
<div anchor="page_media_0"
style="font-size: 20pt; font-family: Arial; position: absolute; overflow: hidden; box-sizing: border-box; width: 90px; height: 30px; top: 762.433px; left: 344.9px; text-align: right; border-width: 1px; border-style: solid;" offset-x="382.6999992370605" offset-y="800.2329992370605">
<b>200265</b>
</div>
This should show 2 boxes which I have selected.
I do Align Objects->align top and get 
which is correct.
If however I start with 
and olign objects->align top, I now get 
The source code was the same in both examples. The only difference is that in the second example the bottom of the page is visible in the design/preview pane. If the bottom of the page is not visible, it behaves as expected.