For the last several years, we have been successfully using the IonCube PHP encoder. It works well, providing us with as secure a solution as we could wish for, for our code. [...] Due to the amount of head pounding involved in finding this issue [where IonCube was removing a valid logic branch], I started to consider using Zend Guard instead, figuring that Zend has far more resources and more experience in this arena, we might see less issues.

He details their upgrade process including comments on the included GUI and how it "just works" (once it's set up)