I believe there's something about the panel pane assigned id `#panels-ipe-paneid-10` that does not agree with the in place editor. These tests were all done in Firefox. Here's how to reproduce:
1) Default Drupal install (7.23)
2) Enable Panels, Panels IPE, and Page manager
3) Create a new variant for the "Node template" (/node/%node) page. I've included importable code, but the important thing is that you have at least 10 panes. We're just trying to generate a pane with the id `#panels-ipe-paneid-10`
4) Save everything and create a basic page node.
5) When viewing the basic page, hit the "Customize this page" button at the bottom.
6) Drag any and all nodes from one region to another. Note that the pane with id `#panels-ipe-paneid-10` will successfully move. --BUT-- it only seems to do so once. If you try to move it from one region to the other and then back again, the placeholder div never appears in the desired new region.
Interestingly enough, if you then move the pane with the "Standard" (not in place) editor, it will successfully work. AND it will successfully work in the IPE on the next page load, but once again, it will only work the first time.
I've tested out a few combinations here. It doesn't seem to matter the position of the pane with with id `#panels-ipe-paneid-10` either on the page or in relative number to other panes (so it's not the problem that this was the last pane created, for example). You can also delete all other panes on the page and still not be able to change the region.
It also doesn't seem to matter what you put in the pane.
I thought it might be because the pane's id ends in a zero, so I added another 10 panes to produce one with id `#panels-ipe-paneid-20` but that works just fine.
The obvious workaround is just to avoid using the 10th pane you create (just recreate it so it gets a later number), but perhaps there's a better fix?