What it looks like is that the s3 plugin and wordpress DO NOT work in parallel in their creation of month based uploads folders.
s3 always uses the current month. In other words, regardless of the publish date of the post, the upload will always get placed in the current month folder (i.e. if today's date is may 2012, I upload an image and it goes to s3bucket/uploads/2012/05/)
By contrast, it seems as though wordpress places the images in the folder based on the date of the original creation of the post. So if you create a post in february save as a draft, then add images in may, then publish it, in s3 your images will be in 2012/05, while in your regular server they will be in 2012/02. This is a serious problem for me for a lot of reasons that are too complex to get into here, but it is a serious issue nonetheless.