Hi Mike, the version of TW3 that you have is the most up to date. I always have issues when publishing in Java and now only use Flash.
I experienced exactly the same issues as you had even hotsposts sometimes dissapearing. It is a shame as the quality of the panos in Java seem to be slightly better than in Flash however on the whole Flash is far more stable.
I know this doesn't help but you have my ear of sympathy :)
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