I am running Logitech's Setpoint. Shutting it down before running calibre-x64 seems to have improved the stability. I just ran calibre for 15 minutes with no problems, while with Setpoint running, it would not last 2 minutes. Setpoint only seems to affect the 64-bit version of calibre; the 32-bit version runs fine. (Setpoint itself is 64-bit.)
Thanks for reminding me to look at the FAQ again. The last time I looked at it I didn't have any Logitech hardware so I completely forgot about the conflict with Setpoint.