There's a possibility that we are experiencing the same issue, have a look at my thread here:
http://boincstats.com/en/forum/18/9222,1
As yet unresolved, but there is a "workaround" by editing the preferences to your liking at one of your projects, BOINC Manager should pay attention to the newest set of preferences. I wasn't sure if this issue was still occurring, but I just got a new laptop and am having the issue with it.
Sounds like the same issue. The problem with your workaround is that there are only three different preference sets available through the project websites (home, work, & school). I have several host-specific preference packages built in BAM. I would have to merge several of my hosts to a single preference package, which is not as nuanced as I require. Looks like I am going to have to write some cc_config files or something. It's frustrating because my hosts are not all in the same location, so I really need remote management.