If you have multiple versions of PHP installed on your system and FPM has been configured for some versions of PHP but not for the other versions / all versions of PHP, then Virtualmin behaves the way you have described.
For example, some websites / virtual servers will offer FPM as an option if the currently selected version of PHP has been configured to use FPM while other websites / virtual servers will not offer FPM as an option under Virtualmin -> Server Configuration -> Website Options: PHP script execution mode.
To use FPM on a particular website / virtual server, you must either change the currently selected version of PHP via Virtualmin -> Server Configuration -> PHP Versions to a version of PHP installed on your system that supports FPM or install FPM for the currently selected version of PHP that you are using.