Ok, here goes.
Let me describe how I use LR. I have 2 catalogs. An "All Pictures" catalog and a "Processing" catalog. I use the processing catalog to import and edit pics. Save changes in xmp is checked in both catalogs. I then export original + xmp and a JPEG. I then copy those 3 files to a directory (manually) in Windows Explorer into the right folder. I then start my "All Pictures" catalog and synchronize the folder (folder is part of the catalog structure). I do this because I do not want be beholden to catalog integrity. I want to have the NEF, XMP and JEPG files and be able to synch them into any other catalog. I realize I lose the edit history doing this. I don't care. I want to be able to reproduce the final result again or make additional changes from the first import.
I recently discovered that if you do that, LR does not respect all the data that is in the XMP from the edit in the "Processing" catalog. It resets the clarity to 0 upon "Add" during the synch process. A few other things change too (Enable Profile Corrections is set to Default instead of Custom).
I lost a lot of subtle changes due to losing the clarity edits.
I found out that if I follow my old process, copy the files, then synch the folder and THEN manually re-add (over write) the altered XMP, I can then get the right settings by selecting "Read Metadata from File".
Anyone else experience this?
I can't really comment on the particulars of your setup, but it seems a little baroque. Have you considered importing the processing catalog, rather than the images? I haven't experimented with this, but I think when you import from a catalog, Lightroom reads the metadata from the database and not from the images. And you are sure that when you import the images into the second catalog you don't have any metadata or develop settings being applied?—I can't tell you how many times I have had metadata or develop settings left over from the last time I imported that I inadvertently applied to the subsequent import.
I would seriously consider trying to do what you need to do with just one catalog.