Why does Adobe have 2 different bookmark icons?

Well here we are... four years later, and I too have been frustrated for a few years with this Bookmark situation as well.  The answer which is given by the "Adobe Community Professionals" doesn't really offer any solution other than create your own Bookmarks; and that has been my only recourse.

But here's the frustrating problem:

I work in Architecture.  Nowadays projects are submitted to govenrning agencies (Building Departments) electronically through a website portal.  Their usual protocol is to combine project applications into one pdf file, plans into one pdf file, and all supplemental materials (pdf documents) into a single pdf file.  Those three separate (combined) pdf files are then uploaded collectively into the job portal. 

So far so good, but now... here is where the issue of bookmarks becomes frustrating:  The Building Department's ePlan protocol requires you to "Set Destination" as "Fit One Full Page"... to every page of the document.   "Fit One Full Page"...  And guess what?  You can only do that "Set Destination" with the (Solid) Bookmarks.  The (Broken) Bookmarks (from merging) don't even give you that option...

So I am forced to replace those (Broken) Bookmarks.  Actually, I create new ones and then move the subset (Solid) Bookmarks under those new (Solid) Bookmark replacements.  I then delete the now unused (Broken) Bookmarks.  This finally allows me "Set Destination" as "Fit One Full Page" to all the Bookmarks.  

For a combined file with many supplemental materials this can get quite tedious, especially if you are presented with a lot of (Broken) Bookmarks.

Adobe is a great product, however if there is one thing I wish they would work on... well, you know.

I know I'm replying to an old thread, but I recently came across this same question and found that there is a difference between the two types of bookmarks you refer to.  The bookmarks that are created manually function just how I imagined all bookmarks function, they bring you to a specific page for easy reference.  The bookmarks that are created by merging pdf's are different in that they are still linked to all the pages their file was associated with.  This provides an advantage if the end user wants to extract those pages they can right-click on that bookmark and extract all pages associated with it.  In my experience that's not a common thing to do, but there is added functionality by having the two types of bookmark.

I would like to know the answer to this as well.  I work in an engineering firm managing 10 spec admins and I work on specs all the time.  Just had a complaint from an engineer on a project that had 4 contracts.  Two admins worked on them to get them out by the due date.  We have about 54 offices and both admins are in two separate offices.  Obviously, one was manually stacking the specs, the other grouped them and stacked all at once, which is how I do it also.  But when the product goes out, it would be nice to fix the icons so they're all consistent and look professional.  So we just need an easy fix; one we are allowed to fix at work without javascript answers since that's not something we are allowed to do.

Double mouse click on the .jar file. It contains Java code, not JavaScript.