Yeah, 6.5 is pretty buggy like that.
Sorry I don't have the answer... but how long of a "test" clip can you export without it screwing up? If you can do 15 minute chunks, maybe you can put them back together in another NLE or compressor and reexport? You'll loose some quality, but at least it'll work...
You're not putting any compression on it, are you? Cause I'd try and make it as close to "raw" as possible and then re-encode with Procoder or something.
I've stopped trying to use Premiere to export web-ready clips- I just whip off a DV master copy (but I'm in NTSC if it makes a difference) and then re-encode somewhere else.