Of course I don't know how you're ripping, but I mostly do so a complete CD at a time, which causes all tracks to be created sequentially. Also, they retain their order when the complete folder they reside in, is dropped into emplode.

I, too, rip entire CD's at a time. And ones where I didn't rename the files are fine. But at one point I redid my directory structure using a tool called Tag&Rename. It apparently created the files in each folder in some bizzare order. I'll never use that tool again. :(

-Dylan