Application Links is not supported by Atlassian. Many customers have reported issues with it, and compatibility varies by point release of Atlassian products.
We recommend you do not install AppLinks. We are working on a 3.0 release of AppLinks which will completely revamp the product. This will be bundled with our products, so you won't need to install it separately. As a bonus, it'll actually work.
Current released version
Application Links 2.1.0 is now available. See the Application Links 2.1 Release Notes