In PEX 2.0 snapshot build 145, calling getKnownSubjects doesn't contain known SubjectCollections, because they haven't been accessed before.
example: call getKnownSubjects(), notice that the key group (SUBJECTS_GROUP) does not exist.
Call getGroupSubjects() and then getKnownSubjects() again. now it's included.

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all pull requests are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.