Some anti-virus/malware programs have a checkbox that reads something like "Do not inform other processes of ........." (hide me). If you check it, the process is hidden from other applications.
Hello, I have Spyware Doctor turned on but Windows reports that my Spyware Dorctor anti virus is off in security center.
This never happens with my Macbook!
That means Windows or other programs cannot detect the presence or activity of that program, so it gets flagged as not running. The program is running in a stealth mode.