Keyword hierarchy corrupted with every export

Why oh why when I export any image from one folder to another do I end up with most keywords applied to that image written to my hierarchical keyword list as a new 1st level keyword and not under the parent keyword as they should be?  I've tried everything. I'm using Windows 7 64 bit, with the latest LR 3.  Export Synonyms, Include on Export, Export containing keywords are all checked with all the keywords and I've unchecked the Write Keywords as Hierarchy in the Export dialogue. With every export I have to clean up my keyword list and I'm at wits end with wasted hours. Any ideas ANYONE? Thanks in advance!

Thanks John for your input.  Your link & explanation of the export
process is helpful.
In reply, Yes, I am using the File>Export command with the option Add to
this Catalog..... for I have been basically putting together photo
submissions to various publishers and creating a Jpeg or Tiff file from
the RAW and keeping the RAW intact in its original folder.  As a result
I have that new file created and sent to a new folder set up for a
particular publisher solely for a record of that submission. (Hope
that's clear)  I've done this with both the "Write Keywords as
Hierarchy" checked and unchecked which appears to get the same results.
Where I think the problem lies primarily is with any synonyms I've
applied to keywords (ie; scientific names for various animal species)
And if I've checked "write keywords as hierarchy" I also end up with a
keyword list in the metadata that includes the top level parent keyword,
which I don't necessarily want visible ( such as the word "Place" along
with "Colorado")   You do mention that synonyms are treated differently....
The synonym Plantea, however, still gets imported as a top-level
keyword, because when you tell LR to export synonyms, it never
includes the parent of the synonym in the file.
Would it be better in order to keep a scientific name in the hierarchy
to instead insert that name under the parent tag in the hierarchy rather
than as a synonym?  Seems like an inadequate use of synonyms per se.
Barb

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