This happens to me too (WordPress 2.3 and 2.6). Not sure if it's exactly the same:
I write a post, add a custom field. When I save or publish it, sometimes the value of the field isn't saved so I have to edit at least one more time. But then when I finally publish it, meaning the Write Post page shows up, the value of the custom field which I added to the previous post shows up on that blank post.
So what happens is the custom field gets filled in the "next" post, not in the "current"/"previous" post I wanted to publish.
This is a bit different from my previous problem that produces multiple draft posts, which was resolved by 2.6 I think.