Hi Fish Pants,
I'm afraid that what you are trying to do is not supported by that patch right now. I didn't remember all the details (it's been over a year since I developed the patch), but after having a look at the code now I know why it isn't working.
The patch only deals with nested enrolments on user login, but not whey you do batch enrolment with enrol_ldap_sync.php. This is because the on login implementation was quite easy (provided the LDAP server had a 'member of' attribute), but batch enrolment was more tricky and I didn't implement it at the time.
The good news is that Moodle 2.0 already has support for nested groups enrolment in both cases (on login and batch). The no so good news is that enrolment code has changed a lot between 1.9 and 2.0, which means that a backport is not as easy as copy & paste, but should be doable if there is enough interest.
Saludos. Iñaki.