Problem with media manager & upload manager

I had a problem with where WP was looking for themes and it IS a bug. I worked around it by some rather tortured symlinking. I have a similar and probably related problem regarding where WP looks for uploads. You configure an uploads directory and sometimes it seems to look there and sometimes it seems to look under the core install. For most installations they would be one and the same and therein lies the issue and why this bug only shows up in setups like mine. I have a compact install, meaning I run five blogs off a single install AND a single database with unique table prefixes and LOTS of symlinks. The flash uploader didn’t work very reliably for me in 2.5.1 but the 2.6.1 one seems to work better. I was a little disappointed that the media library manager doesn’t seem to do thumbnails, however that could be a symtpom of my problem. the flash uploader seems to be putting all uploads into wp-content/uploads in the core install, whereas logically and for ease in management they should go into the separate directories for each blog they belong to. This bug isn’t critical, as I can always just scp the uploads directly to where I want them and not use the uploader. However this doesn’t work for my contributing authors so they have to put it on flickr first or something. If anyone responds to this post I will elaborate, but it doesn’t seem anyone responds to my posts.