I finally found out what is truly causing this issue! Whenever an my anti-virus or CrashPlan software scans my Bootcamp partition, it freezes the system.
I'm not sure if it is a particular file in Windows or if it is just the Bootcamp partition in general, but that is definitely the cause.
After taking the Bootcamp partition off of the backup, CrashPlan works normally.
Does anyone have any ideas on why this is happening?