I believe that:
a. you are reimporting the exported pics back into the LR catalog, either manually or automatically via the "Add to this Catalog" option in the Export window, and
b. the keywords being exported have the option "Export Synonyms" selected.
What's happening is that LR exports the synonyms into the pic's metadata as top-level keywords, with no indication of hierarchy. When the pic is reimported into LR, those top-level keywords get imported into the catalog and attached to the imported pic. (The "Write Keywords as Lightroom Hierarchy" option has nothing to do with this behavior.)
You can stop the synonyms from getting exported and reimported by unchecking the "Export Synonyms" option for each keyword with synonyms. You'll have to do that one keyword at a time -- LR doesn't provide any batch editing of keywords. (I think Rob Cole may have posted a script in these forums to change all your keywords in batch, but I can't find it.)
In general, many people are not very satisfied with LR's synonym features. Please see and vote on this topic in the official Adobe feedback forum:
At the end of the topic is a suggestion to use the Exportant plugin, which may solve your problem.
I suspect John's assessment is right on the money.
The only solutions I know of:
* Resync keywords of exported/added photos with their masters after exporting/importing, e.g. using a plugin like Syncomatic or RelativeAntics (be sure to purge unused keywords from time to time), or
* Use ExportMaster plugin to "auto-resync" them upon export (this functionality has not been ported to Exportant, yet) - won't created unused keywords which need purging.
Neither solution is ideal, but it's either that or don't use synonyms, I guess.
Plugins (easily found using internet search to include plugin name along with author name):
* Syncomatic: John Beardsworth
* RelativeAntics and ExportMaster: me (Rob Cole)
Yes, my situation is exactly the same as you described, I want to manage my exported JPEGs with Lr, so I add them to my catalog.
Thanks a lot John and Rob ... for your advises for the solutions to this situation.
You're welcome Alper - but to be clear, if you are doing these one at a time, there is no need for a plugin, since Lr supports syncing keywords "1 to 1" (or 1 to many) just fine. But if you are doing multiple photos at once, a plugin will come in handy, since Lr has no facility to sync "many to many-related".