In the actual BOINC program (5.10.7) there is an option in the preferences to "switch between applications every "x" minutes". So instead of using a time value to switch between different apps. why not use a percentage value? So the option would read "switch between applications for every "x" percent completed".
This might solve the problem of little projects consuming more of the cpu time and leaving the bigger projects with shorter due dates to expire. And it might help with the fact that I need to manually control (try to at least) how much work from the different projects I get and when, because at this point I have all my work marked as "Won't get new tasks".
Anyways, hope it will at least get considered for the next version of BOINC, or get some other idea sparked.