Perhaps if I called it "joining a split library" the intent would be clearer.
I thought this was a Mac forum. The techniques are mch the same but if we need to get specific it might be better to start your own thread in iTunes for Windows and invite me over there...
When you talk about changing the advanced preference for the media folder location and then consolidating, that leads to a split library. You are moving the media independently of the library files which stay put. If you have started this process but in fact want a portable library then the method I'm suggesting should be relevant.
Admittedly I didn't address the issue of why consolidate didn't copy over some of your content. iTunes can be notably silent when file operations fails so it could be a permissions problem. If you are running Windows then my scripts Unconsolidated and ConsolidateByMoving might be useful. The first can make a playlist of all unconsolidated files, the second can consolidate a selection of files by moving them instead of copying.
Regarding this point... "You can move the library files and the media together if the media folder is a direct subfolder of the library folder." the key factor is the relationship between the objects. When set out correctly you can move the entire iTunes folder as a unit and get iTunes to connect to the database at the new path. Although the absolute path to every file changes, the relative path from library file to media file is unchanged and iTunes effectively does a search and replace for old media path into new media path. I routinely run my iTunes library from E:\iTunes at home and switch to using a freshly updated clone of the same set of files at D:\iTunes when I'm at work. iTunes doesn't even blink at startup to check or correct anything, it just works.
tt2