The update in 0.9.5 resulted in problems with my multi-site install. I have a sub-directory install, and while trying to upload the theme files and wp-include files for the subdirectory site, I kept noticing it was only uploading to the root directories, not my multi-site directory path, plus the other directories (wp-content and wp-includes).

I had to roll back to 0.9.4.1 in order for my multi-site sites to work.

Very disappointing.