How to use panels_bootstrap_layouts?
There a few reason this might be happening

1st is your using a bootstrap 3 theme with bootstrap 2 panel layouts.

The 2nd is your not setting panels with the bootstrap grids width.

After you have choosen the bootstrap stack layout.

1.Click on "Save and update" 

2.Then click on the little gear you will see a drop down menu

3.then click on option that say's "Change"

4.Then select the bootstrap layout option

5.Then you will be able to select the column width of the layout

6.Then save.

Then do the same for the other right or left column and now your column will be right or left. You can see example how to do this here

If you want to hide some panels from on a mobile or desktop display, then you 
need to use bootstrap hide  and show classes which you can find here

1.goto panels gear
2.Select css
3.add the "hidden-lg" class to panels on desktop you want to hide or "hidden-sm hidden-xs" to panels you want to hide on mobile or tablet

I hope that helps