Looking back my guess is that emptying the fields useragent and organization caused this odd behavior, that or it just can't handle a full forum prune. I completely emptied the database of my test board and reinstalled. Its working like it should so I won't change those two fields anymore.
Only one problem that I still have, it won't add the imported messages to the search index. It will only add the messages that were posted via the forum to the search index. Is there anything specific I have to do to enable this?
edit: I've just tried searching on your forum Allan but I can't search on any words from the Guest users. I assume that this feature isn't available yet so I'll just create the gateway on my live forum without a search option for now.