Not sure if this has been documented yet, but sometimes - in fact quite frequently - file manager uploads to a different path than the path I am on. Here's how I noticed and what I know is a work-around that might hold the required clues:
If I am on my hackblog (blog #2) and I click on the Files tab it shows me the files in the hackblog folder. If I then browse and upload a single file it will upload to the weblog folder. Weblog happens to be both blog #1 and my default blog. If I remember it's going to do that then I outsmart it by, upon visiting the Files tab, going to a different folder then back to the hackblog folder.
By the way I do not know if it is showing me the hackblog folder because that is where I was prior to visiting the Files tab, or if that was the last place I was at when I was in the File Manager feature. All I know is if it shows me the hackblog and I upload a file and it uploads to the weblog then something is wrong. Either show me the weblog so I know to click to a different folder, or upload to the path I'm seeing when I click upload.
Okay now back to our regularly scheduled ... er ... was something scheduled for this space?
UPDATE: It is clearly going to the path from the previously selected blog then uploading to the default blog's path. I just had cause to upload something, so I selected blog 9 on the write tab, went to files, saw blog 9's files, uploaded, and found my file in blog 1's path.