pvh, try a couple of sysctls (in sysctl.conf):-

# vm.swappiness controls how aggressively the kernel swaps out inactive processes. Default 50, lower=less quick to swap things out.
vm.swappiness=10

# vm.vfs_cache_pressure controls how fast the kernel reclaims memory used to cache
# copies of inodes and directory entries. Default 100, lower -> slower to reclaim them.
vm.vfs_cache_pressure=10

Reasoning:

1. Boinc is sensitive to its processes being swapped out. (Whether or not its developers agree.)

2. CPDN processes are sensitive to disk timing issues, especially at zip creation time. Keeping core filesystem records in RAM reduces waits for disk access.

These two steps reduced the number of mysterious crashes I had on one of my boxes. I still got a few at zip creation time, though. See next step.

Try changing the disk scheduler to deadline. CFQ is used by default in a lot of distros. CFQ is known to cause problems with some workloads; maybe CPDN and/or BOINC is one. After I changed to deadline, I haven't had any inexplicable crashes. Example code:

# enumerate disks, set scheduler for each
for d in `ls /dev/sd[a-z]`; do
   disk=`basename $d`
   echo deadline > /sys/block/$disk/queue/scheduler
done

You could add this to the kernel command line in your bootloader configuration:

... elevator=deadline ...

(where the dots stand for other stuff already present)

I have reduced swappiness in the .conf file. Do I need to reboot for it to take effect/have to do anything to make the system read the file without rebooting?

Edit: sudo sysctl -p

reads the file once I have modified it.