Membership Plugin update now means things that are negatively protected still show

We are using membership in a bit of a unique way to control access for different groups of people - they have a course level and then course specific information so each person has at least two subscriptions to protect things at the same time.

We'd coordinated it with negative rules using categories and menu. We'd tested it a great deal and it was working fine - with posts marked with categories either showing or not showing based on access level rules. Now the access level hasn't changed but for some reason it's now showing the link for things that are protected. You can click on the link and get "protected content" page warning but the ideal was for those to not even show up in the listing if they'd been protected.

The question is whether this is an issue created by the latest plugin update (3.4.6) which we processed in the last week - we can't figure out why all of a sudden it isn't working as no other settings have been changed.