As discovered in a customer issue:

Subsets of users will see slow performance. Others have everything working just fine. This slowdown happens across all pages within JIRA. The instance has a large number of projects. Users facing slowdown only have access to a small subset of projects. The names of the projects they have access to, are towards the end of the alphabet.

JIRA will complete a permission check when there is a single success. This check is currently performed per project in an alphabetical order. If there is a large number of projects, and the user only has permission to the ones at the end of the alphabet, they will experience slowdown at every permission check (every page).

Workaround

The workaround is to create a bogus project called "A" and add users to the permission scheme here.