TMPGEnc doesn't max out both cores?

I'm using TMPGEnc 3.0 Express to encode something, in the options screen I set everything to multithread, but it still doesn't use all the available cpu power (X2 4600 @ 2.88ghz). How do I make it max out both cores? Right now encoding a 25 min video to wmv format with filters take 2hr30mins, if it maxed out both core I think it could do faster than that. Any suggestions? Thanks.