Which BOINC projects are you having problems with?
Some possible solutions that I can think of.
1. Under preferences, Use at most: 100% of the processors.
2. AQUA is multithreaded, so it will grab both cores of a dual-core machine to run each work unit. You can check that both cores are running (in Windows task manager I think). If all cores are running, then everything should be fine. The current AQUA work units are finishing in about 25-30 hrs on my dual-core.
3. AQUA sometimes doesn't work well with other projects. There is a known problem with cores being left idle.
http://aqua.dwavesys.com/forum_thread.php?id=3364. The latest versions of BOINC might have problems.
Try going back to an earlier version. 6.10.3 is working fine for me.