Actually the problem was that the MS SQL procedure previously had no ORDER BY clause at all, so if it was sorting by upload date that was just happenstance. The feature was intended to sort like a file system and all other db layers had the correct ORDER BY.
Since we are listing folders and files in the same grid, I don't see an easy way to make it sort by upload date since folders don't have upload dates.
My recommendation is to name the files in a way that makes them sort as you would like, ie somefile-2010-03-23.pdf, somefile-2010-03-22.pdf, etc.
Hope it helps,