Trusted root certificate being automatically removed from store

Doing more thorough digging in the Application event log, this entry occured:

Log Name:      Application
Source:        Microsoft-Windows-CAPI2
Date:          24/10/2014 12:49:10
Event ID:      4108
Task Category: None
Level:         Information
Keywords:      Classic
User:          N/A
Computer:      [redacted]
Successful auto delete of third-party root certificate:: Subject [...redacted...]

It turns out that 3rd party root CA's can be deleted by Windows if they are not recognised:

Typically, a certificate is used when you use a secure Web site or when you send and receive secure e-mail. Anyone can issue certificates, but to have transactions that are as secure as possible, certificates must be issued by a trusted certificate authority (CA). Microsoft has included a list in Windows XP and other products of companies and organizations that it considers trusted authorities.