I am concluding that the order in which SEP scans files varies from machine to machine. I do not know why this is. However, when this order causes the scan to attempt to read a file that it cannot view (this will be because it runs as root and is trying to view something not world-readable in a root-squashed directory), it will cause the entire scan to fail.
Root squash is a security feature which is built in to the Linux operating system. It is the default security setting for mounting NFS partitions. The fact that the default setting of a built-in feature causes issues with SEPFL, a program which is meant to improve security, is rather embarrassing.
Update:
In addition to root squash, directories mounted using Samba can also have issues that will cause root to be unable to read files or subdirectories. This will likewise cause the scan to crash.