Problems with grouped and merging layers

Question

Sometimes when I combine layered .pdf files (by dragging pages in or doing Merge Files Into a Single PDF), the layers come in grouped (by file name) and other times they do not. Why is that? Also, is there a way to ungroup layers in Acrobat?
Any help is much appreciated!
For those interested in the background, I have a bunch of layered .pdf files that I want to combine. They were created from a single large Photoshop image sliced into page-sized pieces so the files all have the same layers and the layers are arranged and named the same in every file. I want the combined PDF book to maintain these layers so the user can, with one click, turn on or off a given layer across all pages of the PDF. Clicking on a layer on every page just isn't going to cut it.
I figured I would just combine all of the single PDF pages and then merge all of the layers of a given name so that I end up with just one layer for each type. The problem is that the merging works sometimes and not others. I can't figure out why, but it works far more often when the files combine without the layers grouped. It still doesn't work all of the time, but it NEVER works if the layers come in grouped - so I figure I would start there.
I'm using Adobe Acrobat 9 Pro. I used the method outlined below to turn my layered Photoshop (CS5) files in layered PDF files:
http://www.ehow.com/how_8296095_convert-photoshop-pdf-layers.html

Answer 1

After hours (and hours) of debugging Acrobat, I figured out that as long as the file(s) I drop in are not at the end of the document, then no layer groups are formed - all of the layers in both files are at the top level.
If I drop a file in after all existing pages, then the layers are grouped by file name.
and
If there are layer groups then merging fails. The names of the merged layers disappear from the layer list but the conent is left permanently visible.
If the layers are not divided into groups, then merging works most of the time. I haven't figure out why it occassionaly fails this way too, but so far it's been easy to work around.
This is Adobe Acrobat Pro 9 so no chance of it being fixed - so amybe this will help someone else in the same boat.