I’m not going to say this is you’re problem, but I’ve had similar problems with import tools and WordPress in the past, data being imported to the wrong places. I discovered after a lot of head to keyboard banging that it had nothing to do with WordPress or the import to but with my host. They have XCache installed http://xcache.lighttpd.net/ and I had to disable this before I could do any importing into WP of any kind.
Does your hosting environment have any type of opcode caching running on the server?
