Ntbackup SQL Server Backup Chain Problems

We started having problems with our differential backups failing because the chain to the full backup was invalid. It turns out that something enabled the SQL Server VSS Writer Service, that gives the ntbackup access to backup up SQL Server files. With this service enabled, when ntbackup runs, it logs a "backup event" with sql server and your differential backups no longer have a chain back to your last full backup. The problem is resolved by disabling the SQL Server VSS Writer Service.

Here is the documentation from SQL BOL:

SQL Writer Service: "SQL Writer Service
The SQL Writer Service provides added functionality for backup and restore of SQL Server through the Volume Shadow Copy Service framework.
The SQL Writer Service is installed automatically. It must be running when the Volume Shadow Copy Service (VSS) application requests a backup or restore. To configure the service, use the Microsoft Windows Services applet. The SQL Writer Service installs on all operating systems but is only required on server systems."