Well, this little joke costed me a day. I managed to wreck my network, but I'm not sure how or why. The thing that happened is that the subsites were suddenly no longer accessible. For convenience sake I had created /subsite/wp-admin/uploads folders so that I didn't have to edit all image url when I went from 5 installs to a network. This had always worked fine, but now the subsites gave me 500's and in the end I replaced all images, deleted the subfolders and started editing all image urls afterall... I have no idea what caused this, but the only thing I had been working on was AskApache. After a weekend of work I had rather had not, I am a happy user of 3.5.1 again. No idea if the WP upgrade function returned, but I'll know as soon as I have another upgrade to do than AA :-) The plugin may have become a bit too powerfull.
Oh, and to answer my own initial question, it seems that this plugin changes CHMOD of the upgrades folder. I have changed these rights numerous times, but I noticed that when I had no longer AA installed, the rights were still wrong.